diff --git a/pom.xml b/pom.xml
index 2734743..04109a8 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,10 +3,10 @@
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>com.milaboratory</groupId>
-    <artifactId>migec2</artifactId>
+    <artifactId>oncomigec</artifactId>
     <version>1.0-SNAPSHOT</version>
     <packaging>jar</packaging>
-    <name>MIGEC2</name>
+    <name>OncoMIGEC</name>
 
     <repositories>
         <repository>
@@ -167,7 +167,7 @@
                 <configuration>
                     <archive>
                         <manifest>
-                            <mainClass>com.milaboratory.migec2.pipeline.MigecCli</mainClass>
+                            <mainClass>com.milaboratory.oncomigec.pipeline.MigecCli</mainClass>
                             <addDefaultImplementationEntries>
                                 true
                             </addDefaultImplementationEntries>
@@ -228,7 +228,7 @@
                                 </transformer>
                                 <transformer
                                         implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                                    <mainClass>com.milaboratory.migec2.pipeline.MigecCli</mainClass>
+                                    <mainClass>com.milaboratory.oncomigec.pipeline.MigecCli</mainClass>
                                 </transformer>
                             </transformers>
                             <shadedArtifactAttached>true</shadedArtifactAttached>
diff --git a/src/main/groovy/com/milaboratory/migec2/model/classifier/TrainClassifier.groovy b/src/main/groovy/com/milaboratory/oncomigec/model/classifier/TrainClassifier.groovy
similarity index 97%
rename from src/main/groovy/com/milaboratory/migec2/model/classifier/TrainClassifier.groovy
rename to src/main/groovy/com/milaboratory/oncomigec/model/classifier/TrainClassifier.groovy
index ab6a9e8..86c39c8 100644
--- a/src/main/groovy/com/milaboratory/migec2/model/classifier/TrainClassifier.groovy
+++ b/src/main/groovy/com/milaboratory/oncomigec/model/classifier/TrainClassifier.groovy
@@ -16,10 +16,10 @@
  * Last modified on 23.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.classifier
+package com.milaboratory.oncomigec.model.classifier
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet
-import com.milaboratory.migec2.model.variant.Variant
+import com.milaboratory.oncomigec.model.variant.Variant
 import weka.core.Instance
 
 def cli = new CliBuilder(usage: "TrainClassifier [options] control_variants input_vardump output_prefix\n" +
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java b/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java
deleted file mode 100644
index 54ffaa6..0000000
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package com.milaboratory.migec2.core.align.processor;
-
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-
-public interface AlignerFactory <T extends Aligner> {
-    public T fromReferenceLibrary(ReferenceLibrary referenceLibrary);
-}
diff --git a/src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java b/src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java
deleted file mode 100644
index de4acee..0000000
--- a/src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java
+++ /dev/null
@@ -1,4 +0,0 @@
-package com.milaboratory.migec2.core.align.reference;
-
-public class KmerLibrary {
-}
diff --git a/src/main/java/com/milaboratory/migec2/core/align/entity/PAlignmentResult.java b/src/main/java/com/milaboratory/oncomigec/core/align/entity/PAlignmentResult.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/core/align/entity/PAlignmentResult.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/entity/PAlignmentResult.java
index 54bea2e..4212eb2 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/entity/PAlignmentResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/entity/PAlignmentResult.java
@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.entity;
+package com.milaboratory.oncomigec.core.align.entity;
 
 import com.milaboratory.core.sequence.Range;
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 import java.util.List;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/align/entity/SAlignmentResult.java b/src/main/java/com/milaboratory/oncomigec/core/align/entity/SAlignmentResult.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/align/entity/SAlignmentResult.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/entity/SAlignmentResult.java
index 958d838..389a427 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/entity/SAlignmentResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/entity/SAlignmentResult.java
@@ -13,13 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.entity;
+package com.milaboratory.oncomigec.core.align.entity;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinder.java b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinder.java
similarity index 94%
rename from src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinder.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinder.java
index f544be9..d8f5d59 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinder.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinder.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 import com.milaboratory.util.IntArrayList;
 
 public class KMerFinder {
diff --git a/src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinderResult.java b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderResult.java
similarity index 77%
rename from src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinderResult.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderResult.java
index 47b1b7c..e41ea44 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinderResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderResult.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 public class KMerFinderResult {
     private final double information;
diff --git a/src/main/java/com/milaboratory/migec2/core/align/kmer/KmerMap.java b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerMap.java
similarity index 99%
rename from src/main/java/com/milaboratory/migec2/core/align/kmer/KmerMap.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerMap.java
index 49dbcc2..2be8967 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/kmer/KmerMap.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerMap.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
 //
 // Adapted from KAnalyze package, see
diff --git a/src/main/java/com/milaboratory/migec2/core/align/kmer/KmerUtils.java b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerUtils.java
similarity index 90%
rename from src/main/java/com/milaboratory/migec2/core/align/kmer/KmerUtils.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerUtils.java
index 9f7fcb7..3056047 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/kmer/KmerUtils.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerUtils.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public class KmerUtils {
     private final int k;
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/Aligner.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/Aligner.java
similarity index 88%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/Aligner.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/Aligner.java
index f9e9470..c8933a2 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/Aligner.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/Aligner.java
@@ -13,12 +13,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.processor;
+package com.milaboratory.oncomigec.core.align.processor;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.entity.PAlignmentResult;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public interface Aligner {
     /**
diff --git a/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java
new file mode 100644
index 0000000..eb53b37
--- /dev/null
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java
@@ -0,0 +1,7 @@
+package com.milaboratory.oncomigec.core.align.processor;
+
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+
+public interface AlignerFactory <T extends Aligner> {
+    public T fromReferenceLibrary(ReferenceLibrary referenceLibrary);
+}
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactoryWithReference.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactoryWithReference.java
similarity index 78%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactoryWithReference.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactoryWithReference.java
index 8df9e0b..4eb9e96 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactoryWithReference.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactoryWithReference.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.align.processor;
+package com.milaboratory.oncomigec.core.align.processor;
 
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public class AlignerFactoryWithReference<T extends Aligner> {
     private final ReferenceLibrary referenceLibrary;
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/AlignmentEvaluator.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignmentEvaluator.java
similarity index 92%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/AlignmentEvaluator.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignmentEvaluator.java
index 1067045..ef7e3e8 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/AlignmentEvaluator.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignmentEvaluator.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/DummyAlignmentEvaluator.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/DummyAlignmentEvaluator.java
similarity index 93%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/DummyAlignmentEvaluator.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/DummyAlignmentEvaluator.java
index 0cfa8cd..855e78d 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/DummyAlignmentEvaluator.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/DummyAlignmentEvaluator.java
@@ -16,7 +16,7 @@
  * Last modified on 19.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAligner.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAligner.java
similarity index 83%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAligner.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAligner.java
index 3f203c4..e7bf15d 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAligner.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAligner.java
@@ -1,17 +1,17 @@
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.alignment.AffineGapAlignmentScoring;
 import com.milaboratory.core.sequence.alignment.LocalAligner;
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.entity.PAlignmentResult;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.kmer.KMerFinder;
-import com.milaboratory.migec2.core.align.kmer.KMerFinderResult;
-import com.milaboratory.migec2.core.align.processor.Aligner;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.kmer.KMerFinder;
+import com.milaboratory.oncomigec.core.align.kmer.KMerFinderResult;
+import com.milaboratory.oncomigec.core.align.processor.Aligner;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAlignerFactory.java
similarity index 82%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAlignerFactory.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAlignerFactory.java
index e81322d..ad439c1 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAlignerFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAlignerFactory.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
-import com.milaboratory.migec2.core.align.processor.AlignerFactory;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactory;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public class ExtendedExomeAlignerFactory implements AlignerFactory<ExtendedExomeAligner> {
     private final int k;
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/LocalAlignmentEvaluator.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/LocalAlignmentEvaluator.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/LocalAlignmentEvaluator.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/LocalAlignmentEvaluator.java
index 959cc45..1a404e1 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/LocalAlignmentEvaluator.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/LocalAlignmentEvaluator.java
@@ -14,10 +14,9 @@
  * limitations under the License.
  */
 
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
-import com.milaboratory.core.sequence.aminoacid.AminoAcidAlphabet;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAligner.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAligner.java
similarity index 89%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAligner.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAligner.java
index c788663..2093566 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAligner.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAligner.java
@@ -13,16 +13,16 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.alignment.*;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.entity.PAlignmentResult;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.processor.Aligner;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.processor.Aligner;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAlignerFactory.java
similarity index 85%
rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAlignerFactory.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAlignerFactory.java
index 959d4f7..82a8d56 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAlignerFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAlignerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.alignment.KAlignerParameters;
-import com.milaboratory.migec2.core.align.processor.AlignerFactory;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactory;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 public class SimpleExomeAlignerFactory implements AlignerFactory<SimpleExomeAligner> {
     private final KAlignerParameters parameters;
diff --git a/src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java
new file mode 100644
index 0000000..d760d5d
--- /dev/null
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java
@@ -0,0 +1,4 @@
+package com.milaboratory.oncomigec.core.align.reference;
+
+public class KmerLibrary {
+}
diff --git a/src/main/java/com/milaboratory/migec2/core/align/reference/Reference.java b/src/main/java/com/milaboratory/oncomigec/core/align/reference/Reference.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/align/reference/Reference.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/reference/Reference.java
index fe5cb91..510b127 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/reference/Reference.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/reference/Reference.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.reference;
+package com.milaboratory.oncomigec.core.align.reference;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/align/reference/ReferenceLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/align/reference/ReferenceLibrary.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/core/align/reference/ReferenceLibrary.java
rename to src/main/java/com/milaboratory/oncomigec/core/align/reference/ReferenceLibrary.java
index f7f6553..72c37fe 100644
--- a/src/main/java/com/milaboratory/migec2/core/align/reference/ReferenceLibrary.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/align/reference/ReferenceLibrary.java
@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.reference;
+package com.milaboratory.oncomigec.core.align.reference;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.Util;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/entity/Consensus.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/Consensus.java
similarity index 71%
rename from src/main/java/com/milaboratory/migec2/core/assemble/entity/Consensus.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/entity/Consensus.java
index e28f7bc..279939d 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/entity/Consensus.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/Consensus.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.assemble.entity;
+package com.milaboratory.oncomigec.core.assemble.entity;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.QualityHistogram;
+import com.milaboratory.oncomigec.util.QualityHistogram;
 
 public interface Consensus {
     public int size();
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/entity/PConsensus.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/PConsensus.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/core/assemble/entity/PConsensus.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/entity/PConsensus.java
index d9567ff..9497c89 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/entity/PConsensus.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/PConsensus.java
@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.assemble.entity;
+package com.milaboratory.oncomigec.core.assemble.entity;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.QualityHistogram;
+import com.milaboratory.oncomigec.util.QualityHistogram;
 
 public final class PConsensus implements Consensus {
     private final SConsensus consensus1, consensus2;
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/entity/SConsensus.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/SConsensus.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/core/assemble/entity/SConsensus.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/entity/SConsensus.java
index 1b9d621..add5adf 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/entity/SConsensus.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/SConsensus.java
@@ -13,12 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.assemble.entity;
+package com.milaboratory.oncomigec.core.assemble.entity;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.QualityHistogram;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.QualityHistogram;
 
 import java.util.List;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerFactory.java
similarity index 60%
rename from src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerFactory.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerFactory.java
index 4bf5398..6360a73 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.assemble.misc;
+package com.milaboratory.oncomigec.core.assemble.misc;
 
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.assemble.processor.Assembler;
-import com.milaboratory.migec2.core.io.entity.Mig;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.assemble.processor.Assembler;
+import com.milaboratory.oncomigec.core.io.entity.Mig;
 
 public abstract class AssemblerFactory<T extends Consensus, V extends Mig> {
     protected final AssemblerParameters parameters;
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerParameters.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerParameters.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerParameters.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerParameters.java
index 997446d..b68a6bf 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerParameters.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerParameters.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.assemble.misc;
+package com.milaboratory.oncomigec.core.assemble.misc;
 
-import com.milaboratory.migec2.util.ParameterSet;
+import com.milaboratory.oncomigec.util.ParameterSet;
 import org.jdom.Element;
 
 public final class AssemblerParameters implements ParameterSet {
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/misc/PAssemblerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/PAssemblerFactory.java
similarity index 56%
rename from src/main/java/com/milaboratory/migec2/core/assemble/misc/PAssemblerFactory.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/misc/PAssemblerFactory.java
index c4d5261..ad15dde 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/misc/PAssemblerFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/PAssemblerFactory.java
@@ -1,9 +1,9 @@
-package com.milaboratory.migec2.core.assemble.misc;
+package com.milaboratory.oncomigec.core.assemble.misc;
 
-import com.milaboratory.migec2.core.assemble.entity.PConsensus;
-import com.milaboratory.migec2.core.assemble.processor.PAssembler;
-import com.milaboratory.migec2.core.assemble.processor.SAssembler;
-import com.milaboratory.migec2.core.io.entity.PMig;
+import com.milaboratory.oncomigec.core.assemble.entity.PConsensus;
+import com.milaboratory.oncomigec.core.assemble.processor.PAssembler;
+import com.milaboratory.oncomigec.core.assemble.processor.SAssembler;
+import com.milaboratory.oncomigec.core.io.entity.PMig;
 
 public final class PAssemblerFactory extends AssemblerFactory<PConsensus, PMig> {
 
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/misc/SAssemblerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/SAssemblerFactory.java
similarity index 59%
rename from src/main/java/com/milaboratory/migec2/core/assemble/misc/SAssemblerFactory.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/misc/SAssemblerFactory.java
index bb0273d..7014407 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/misc/SAssemblerFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/SAssemblerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.assemble.misc;
+package com.milaboratory.oncomigec.core.assemble.misc;
 
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.assemble.processor.SAssembler;
-import com.milaboratory.migec2.core.io.entity.SMig;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.assemble.processor.SAssembler;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
 
 public final class SAssemblerFactory extends AssemblerFactory<SConsensus, SMig> {
 
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/processor/Assembler.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/Assembler.java
similarity index 91%
rename from src/main/java/com/milaboratory/migec2/core/assemble/processor/Assembler.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/processor/Assembler.java
index 6c6c70a..a35ea44 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/processor/Assembler.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/Assembler.java
@@ -13,13 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.assemble.processor;
+package com.milaboratory.oncomigec.core.assemble.processor;
 
 import cc.redberry.pipe.Processor;
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.io.entity.Mig;
-import com.milaboratory.migec2.util.ProcessorResultWrapper;
-import com.milaboratory.migec2.util.QualityHistogram;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.io.entity.Mig;
+import com.milaboratory.oncomigec.util.ProcessorResultWrapper;
+import com.milaboratory.oncomigec.util.QualityHistogram;
 
 import java.util.Collections;
 import java.util.LinkedList;
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/processor/PAssembler.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/PAssembler.java
similarity index 88%
rename from src/main/java/com/milaboratory/migec2/core/assemble/processor/PAssembler.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/processor/PAssembler.java
index dfaf41d..15d86ee 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/processor/PAssembler.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/PAssembler.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.assemble.processor;
+package com.milaboratory.oncomigec.core.assemble.processor;
 
-import com.milaboratory.migec2.core.assemble.entity.PConsensus;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.io.entity.PMig;
+import com.milaboratory.oncomigec.core.assemble.entity.PConsensus;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.io.entity.PMig;
 
 public final class PAssembler extends Assembler<PConsensus, PMig> {
     private final SAssembler assembler1, assembler2;
diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/processor/SAssembler.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/SAssembler.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/assemble/processor/SAssembler.java
rename to src/main/java/com/milaboratory/oncomigec/core/assemble/processor/SAssembler.java
index c327727..a9301c2 100644
--- a/src/main/java/com/milaboratory/migec2/core/assemble/processor/SAssembler.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/SAssembler.java
@@ -1,14 +1,14 @@
-package com.milaboratory.migec2.core.assemble.processor;
+package com.milaboratory.oncomigec.core.assemble.processor;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceBuilder;
 import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.assemble.misc.AssemblerParameters;
-import com.milaboratory.migec2.core.io.entity.SMig;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.assemble.misc.AssemblerParameters;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
+import com.milaboratory.oncomigec.util.Util;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignedConsensus.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignedConsensus.java
similarity index 92%
rename from src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignedConsensus.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignedConsensus.java
index 3af8bc0..c3ea99d 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignedConsensus.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignedConsensus.java
@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.consalign.entity;
+package com.milaboratory.oncomigec.core.consalign.entity;
 
 import com.milaboratory.core.sequence.Range;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.mutations.MigecMutationsCollection;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection;
 
 import java.util.List;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignerReferenceLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignerReferenceLibrary.java
similarity index 84%
rename from src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignerReferenceLibrary.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignerReferenceLibrary.java
index e96a744..cd6f8cc 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignerReferenceLibrary.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignerReferenceLibrary.java
@@ -13,18 +13,17 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.consalign.entity;
+package com.milaboratory.oncomigec.core.consalign.entity;
 
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage;
-import com.milaboratory.migec2.core.mutations.MigecMutationsCollection;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage;
+import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection;
 
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Set;
 
 public final class AlignerReferenceLibrary {
     private final Map<Reference, MutationsAndCoverage> mutationsAndCoverageByReference =
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerFactory.java
similarity index 66%
rename from src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerFactory.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerFactory.java
index 71d488e..05c2378 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.consalign.misc;
+package com.milaboratory.oncomigec.core.consalign.misc;
 
-import com.milaboratory.migec2.core.align.processor.AlignerFactoryWithReference;
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.consalign.processor.ConsensusAligner;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactoryWithReference;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.consalign.processor.ConsensusAligner;
 
 public abstract class ConsensusAlignerFactory<T extends Consensus> {
     protected final AlignerFactoryWithReference alignerFactory;
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerParameters.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerParameters.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerParameters.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerParameters.java
index 5044844..3fc9d6f 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerParameters.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerParameters.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.consalign.misc;
+package com.milaboratory.oncomigec.core.consalign.misc;
 
-import com.milaboratory.migec2.util.ParameterSet;
+import com.milaboratory.oncomigec.util.ParameterSet;
 import org.jdom.Element;
 
 public final class ConsensusAlignerParameters implements ParameterSet {
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/misc/PConsensusAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/PConsensusAlignerFactory.java
similarity index 66%
rename from src/main/java/com/milaboratory/migec2/core/consalign/misc/PConsensusAlignerFactory.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/misc/PConsensusAlignerFactory.java
index 50d4260..63083f3 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/misc/PConsensusAlignerFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/PConsensusAlignerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.consalign.misc;
+package com.milaboratory.oncomigec.core.consalign.misc;
 
-import com.milaboratory.migec2.core.align.processor.AlignerFactoryWithReference;
-import com.milaboratory.migec2.core.assemble.entity.PConsensus;
-import com.milaboratory.migec2.core.consalign.processor.PConsensusAligner;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactoryWithReference;
+import com.milaboratory.oncomigec.core.assemble.entity.PConsensus;
+import com.milaboratory.oncomigec.core.consalign.processor.PConsensusAligner;
 
 public final class PConsensusAlignerFactory extends ConsensusAlignerFactory<PConsensus> {
 
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/misc/SConsensusAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/SConsensusAlignerFactory.java
similarity index 66%
rename from src/main/java/com/milaboratory/migec2/core/consalign/misc/SConsensusAlignerFactory.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/misc/SConsensusAlignerFactory.java
index b3da769..5354234 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/misc/SConsensusAlignerFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/SConsensusAlignerFactory.java
@@ -1,8 +1,8 @@
-package com.milaboratory.migec2.core.consalign.misc;
+package com.milaboratory.oncomigec.core.consalign.misc;
 
-import com.milaboratory.migec2.core.align.processor.AlignerFactoryWithReference;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.consalign.processor.SConsensusAligner;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactoryWithReference;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.consalign.processor.SConsensusAligner;
 
 public final class SConsensusAlignerFactory extends ConsensusAlignerFactory<SConsensus> {
 
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationQualityPair.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationQualityPair.java
similarity index 86%
rename from src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationQualityPair.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationQualityPair.java
index 49a60cc..2ae7191 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationQualityPair.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationQualityPair.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.consalign.mutations;
+package com.milaboratory.oncomigec.core.consalign.mutations;
 
 public class MutationQualityPair {
     private final int mutationCode;
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsAndCoverage.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsAndCoverage.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsAndCoverage.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsAndCoverage.java
index f899b5e..4564eb9 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsAndCoverage.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsAndCoverage.java
@@ -13,17 +13,17 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.consalign.mutations;
+package com.milaboratory.oncomigec.core.consalign.mutations;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.mutations.MigecMutation;
-import com.milaboratory.migec2.core.mutations.MigecMutationsCollection;
-import com.milaboratory.migec2.util.Basics;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.mutations.MigecMutation;
+import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection;
+import com.milaboratory.oncomigec.util.Basics;
 
 import java.util.HashSet;
 import java.util.Map;
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractor.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractor.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractor.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractor.java
index 6bc98eb..baf8470 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractor.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractor.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.consalign.mutations;
+package com.milaboratory.oncomigec.core.consalign.mutations;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.alignment.KAligner;
@@ -8,10 +8,10 @@
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters;
-import com.milaboratory.migec2.core.mutations.MigecMutationsCollection;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters;
+import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection;
 
 import java.util.*;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/NucleotideCoverage.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/NucleotideCoverage.java
similarity index 98%
rename from src/main/java/com/milaboratory/migec2/core/consalign/mutations/NucleotideCoverage.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/NucleotideCoverage.java
index d6bb28d..7a75a65 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/NucleotideCoverage.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/NucleotideCoverage.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.consalign.mutations;
+package com.milaboratory.oncomigec.core.consalign.mutations;
 
 import java.util.concurrent.atomic.AtomicIntegerArray;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAligner.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAligner.java
similarity index 79%
rename from src/main/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAligner.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAligner.java
index ccc0c21..2cd5695 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAligner.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAligner.java
@@ -13,15 +13,15 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.consalign.processor;
+package com.milaboratory.oncomigec.core.consalign.processor;
 
 import cc.redberry.pipe.Processor;
-import com.milaboratory.migec2.core.align.processor.Aligner;
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters;
-import com.milaboratory.migec2.util.ProcessorResultWrapper;
+import com.milaboratory.oncomigec.core.align.processor.Aligner;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary;
+import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters;
+import com.milaboratory.oncomigec.util.ProcessorResultWrapper;
 
 public abstract class ConsensusAligner<T extends Consensus> implements Processor<ProcessorResultWrapper<T>,
         ProcessorResultWrapper<AlignedConsensus>> {
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/processor/PConsensusAligner.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/PConsensusAligner.java
similarity index 87%
rename from src/main/java/com/milaboratory/migec2/core/consalign/processor/PConsensusAligner.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/processor/PConsensusAligner.java
index 98e8a3d..b49900c 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/processor/PConsensusAligner.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/PConsensusAligner.java
@@ -1,16 +1,16 @@
-package com.milaboratory.migec2.core.consalign.processor;
+package com.milaboratory.oncomigec.core.consalign.processor;
 
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
-import com.milaboratory.migec2.core.align.entity.PAlignmentResult;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.processor.Aligner;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.assemble.entity.PConsensus;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters;
-import com.milaboratory.migec2.core.consalign.mutations.MutationsExtractor;
-import com.milaboratory.migec2.core.mutations.MigecMutationsCollection;
+import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.processor.Aligner;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.assemble.entity.PConsensus;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters;
+import com.milaboratory.oncomigec.core.consalign.mutations.MutationsExtractor;
+import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/processor/SConsensusAligner.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/SConsensusAligner.java
similarity index 78%
rename from src/main/java/com/milaboratory/migec2/core/consalign/processor/SConsensusAligner.java
rename to src/main/java/com/milaboratory/oncomigec/core/consalign/processor/SConsensusAligner.java
index dca5a82..8c3f68f 100644
--- a/src/main/java/com/milaboratory/migec2/core/consalign/processor/SConsensusAligner.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/SConsensusAligner.java
@@ -1,14 +1,14 @@
-package com.milaboratory.migec2.core.consalign.processor;
+package com.milaboratory.oncomigec.core.consalign.processor;
 
 import com.milaboratory.core.sequence.alignment.LocalAlignment;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.processor.Aligner;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters;
-import com.milaboratory.migec2.core.consalign.mutations.MutationsExtractor;
-import com.milaboratory.migec2.core.mutations.MigecMutationsCollection;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.processor.Aligner;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters;
+import com.milaboratory.oncomigec.core.consalign.mutations.MutationsExtractor;
+import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/src/main/java/com/milaboratory/migec2/core/correct/CorrectedConsensus.java b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectedConsensus.java
similarity index 93%
rename from src/main/java/com/milaboratory/migec2/core/correct/CorrectedConsensus.java
rename to src/main/java/com/milaboratory/oncomigec/core/correct/CorrectedConsensus.java
index 44b356d..4c22825 100644
--- a/src/main/java/com/milaboratory/migec2/core/correct/CorrectedConsensus.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectedConsensus.java
@@ -13,17 +13,17 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.correct;
+package com.milaboratory.oncomigec.core.correct;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.haplotype.Haplotype;
-import com.milaboratory.migec2.core.mutations.MutationDifference;
-import com.milaboratory.migec2.core.mutations.wrappers.MutationWrapperCollection;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.haplotype.Haplotype;
+import com.milaboratory.oncomigec.core.mutations.MutationDifference;
+import com.milaboratory.oncomigec.core.mutations.wrappers.MutationWrapperCollection;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/src/main/java/com/milaboratory/migec2/core/correct/Corrector.java b/src/main/java/com/milaboratory/oncomigec/core/correct/Corrector.java
similarity index 89%
rename from src/main/java/com/milaboratory/migec2/core/correct/Corrector.java
rename to src/main/java/com/milaboratory/oncomigec/core/correct/Corrector.java
index f197939..e7458b5 100644
--- a/src/main/java/com/milaboratory/migec2/core/correct/Corrector.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/correct/Corrector.java
@@ -13,16 +13,16 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.correct;
+package com.milaboratory.oncomigec.core.correct;
 
 import com.milaboratory.core.sequence.Range;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary;
-import com.milaboratory.migec2.core.mutations.MigecMutation;
-import com.milaboratory.migec2.core.mutations.MigecMutationsCollection;
-import com.milaboratory.migec2.model.classifier.BaseVariantClassifier;
-import com.milaboratory.migec2.model.classifier.VariantClassifier;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary;
+import com.milaboratory.oncomigec.core.mutations.MigecMutation;
+import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection;
+import com.milaboratory.oncomigec.model.classifier.BaseVariantClassifier;
+import com.milaboratory.oncomigec.model.classifier.VariantClassifier;
 
 import java.util.HashSet;
 import java.util.Set;
diff --git a/src/main/java/com/milaboratory/migec2/core/correct/CorrectorParameters.java b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/correct/CorrectorParameters.java
rename to src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java
index 2bcae95..a7794d0 100644
--- a/src/main/java/com/milaboratory/migec2/core/correct/CorrectorParameters.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.correct;
+package com.milaboratory.oncomigec.core.correct;
 
-import com.milaboratory.migec2.util.ParameterSet;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.ParameterSet;
+import com.milaboratory.oncomigec.util.Util;
 import org.jdom.Element;
 
 public final class CorrectorParameters implements ParameterSet {
diff --git a/src/main/java/com/milaboratory/migec2/core/correct/CorrectorReferenceLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorReferenceLibrary.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/core/correct/CorrectorReferenceLibrary.java
rename to src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorReferenceLibrary.java
index 3aaea3d..73acafb 100644
--- a/src/main/java/com/milaboratory/migec2/core/correct/CorrectorReferenceLibrary.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorReferenceLibrary.java
@@ -13,18 +13,18 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.correct;
+package com.milaboratory.oncomigec.core.correct;
 
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary;
-import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage;
-import com.milaboratory.migec2.model.classifier.ClassifierResult;
-import com.milaboratory.migec2.model.classifier.VariantClassifier;
-import com.milaboratory.migec2.model.variant.Variant;
-import com.milaboratory.migec2.model.variant.VariantContainer;
-import com.milaboratory.migec2.model.variant.VariantLibrary;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary;
+import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage;
+import com.milaboratory.oncomigec.model.classifier.ClassifierResult;
+import com.milaboratory.oncomigec.model.classifier.VariantClassifier;
+import com.milaboratory.oncomigec.model.variant.Variant;
+import com.milaboratory.oncomigec.model.variant.VariantContainer;
+import com.milaboratory.oncomigec.model.variant.VariantLibrary;
 
 import java.util.*;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/correct/MutationFilter.java b/src/main/java/com/milaboratory/oncomigec/core/correct/MutationFilter.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/correct/MutationFilter.java
rename to src/main/java/com/milaboratory/oncomigec/core/correct/MutationFilter.java
index 8423f9b..1ace036 100644
--- a/src/main/java/com/milaboratory/migec2/core/correct/MutationFilter.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/correct/MutationFilter.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.correct;
+package com.milaboratory.oncomigec.core.correct;
 
 import java.util.Set;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/haplotype/Haplotype.java b/src/main/java/com/milaboratory/oncomigec/core/haplotype/Haplotype.java
similarity index 94%
rename from src/main/java/com/milaboratory/migec2/core/haplotype/Haplotype.java
rename to src/main/java/com/milaboratory/oncomigec/core/haplotype/Haplotype.java
index 3907cef..4817593 100644
--- a/src/main/java/com/milaboratory/migec2/core/haplotype/Haplotype.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/haplotype/Haplotype.java
@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.haplotype;
+package com.milaboratory.oncomigec.core.haplotype;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.correct.CorrectedConsensus;
-import com.milaboratory.migec2.core.mutations.MutationDifference;
+import com.milaboratory.oncomigec.core.correct.CorrectedConsensus;
+import com.milaboratory.oncomigec.core.mutations.MutationDifference;
 
 import java.util.List;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeCounters.java b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeCounters.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeCounters.java
rename to src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeCounters.java
index 0e18606..64c0007 100644
--- a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeCounters.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeCounters.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.haplotype;
+package com.milaboratory.oncomigec.core.haplotype;
 
 public final class HaplotypeCounters {
     private int count = 0, readCount = 0;
diff --git a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTree.java b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTree.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTree.java
rename to src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTree.java
index 2cbb7fa..a66e131 100644
--- a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTree.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTree.java
@@ -13,15 +13,15 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.haplotype;
+package com.milaboratory.oncomigec.core.haplotype;
 
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.correct.CorrectedConsensus;
-import com.milaboratory.migec2.core.correct.CorrectorReferenceLibrary;
-import com.milaboratory.migec2.core.mutations.MutationDifference;
-import com.milaboratory.migec2.model.variant.VariantLibrary;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.correct.CorrectedConsensus;
+import com.milaboratory.oncomigec.core.correct.CorrectorReferenceLibrary;
+import com.milaboratory.oncomigec.core.mutations.MutationDifference;
+import com.milaboratory.oncomigec.model.variant.VariantLibrary;
 import org.apache.commons.math.MathException;
 import org.apache.commons.math.distribution.BinomialDistribution;
 import org.apache.commons.math.distribution.BinomialDistributionImpl;
diff --git a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeParameters.java b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeParameters.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeParameters.java
rename to src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeParameters.java
index b3d8f40..1797576 100644
--- a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeParameters.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeParameters.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.haplotype;
+package com.milaboratory.oncomigec.core.haplotype;
 
-import com.milaboratory.migec2.util.ParameterSet;
+import com.milaboratory.oncomigec.util.ParameterSet;
 import org.jdom.Element;
 
 public final class HaplotypeTreeParameters implements ParameterSet {
diff --git a/src/main/java/com/milaboratory/migec2/core/io/entity/Mig.java b/src/main/java/com/milaboratory/oncomigec/core/io/entity/Mig.java
similarity index 94%
rename from src/main/java/com/milaboratory/migec2/core/io/entity/Mig.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/entity/Mig.java
index 774c077..f022cc7 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/entity/Mig.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/entity/Mig.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.io.entity;
+package com.milaboratory.oncomigec.core.io.entity;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/io/entity/PMig.java b/src/main/java/com/milaboratory/oncomigec/core/io/entity/PMig.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/io/entity/PMig.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/entity/PMig.java
index 3932f6f..120fa22 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/entity/PMig.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/entity/PMig.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.io.entity;
+package com.milaboratory.oncomigec.core.io.entity;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/io/entity/SMig.java b/src/main/java/com/milaboratory/oncomigec/core/io/entity/SMig.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/core/io/entity/SMig.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/entity/SMig.java
index 27004f4..7098639 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/entity/SMig.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/entity/SMig.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.io.entity;
+package com.milaboratory.oncomigec.core.io.entity;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/MigReaderParameters.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/MigReaderParameters.java
similarity index 94%
rename from src/main/java/com/milaboratory/migec2/core/io/misc/MigReaderParameters.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/MigReaderParameters.java
index 0f12305..5ca4da2 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/misc/MigReaderParameters.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/MigReaderParameters.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.core.io.misc;
+package com.milaboratory.oncomigec.core.io.misc;
 
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.Util;
 
 public class MigReaderParameters {
     private final byte umiQualThreshold;
diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/ReadInfo.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/ReadInfo.java
similarity index 91%
rename from src/main/java/com/milaboratory/migec2/core/io/misc/ReadInfo.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/ReadInfo.java
index b4276b4..fb63059 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/misc/ReadInfo.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/ReadInfo.java
@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.io.misc;
+package com.milaboratory.oncomigec.core.io.misc;
 
 import com.milaboratory.core.sequencing.read.SequencingRead;
-import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult;
 
 public class ReadInfo<ReadType extends SequencingRead> {
     private final ReadType read;
diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/UmiHistogram.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogram.java
similarity index 99%
rename from src/main/java/com/milaboratory/migec2/core/io/misc/UmiHistogram.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogram.java
index 74a2ddd..b8bb86b 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/misc/UmiHistogram.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogram.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.io.misc;
+package com.milaboratory.oncomigec.core.io.misc;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.util.Bit2Array;
diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/index/IndexingInfo.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/index/IndexingInfo.java
similarity index 89%
rename from src/main/java/com/milaboratory/migec2/core/io/misc/index/IndexingInfo.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/index/IndexingInfo.java
index e86c4c7..f6f78c8 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/misc/index/IndexingInfo.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/index/IndexingInfo.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.io.misc.index;
+package com.milaboratory.oncomigec.core.io.misc.index;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.io.misc.ReadInfo;
+import com.milaboratory.oncomigec.core.io.misc.ReadInfo;
 
 public class IndexingInfo {
     private final ReadInfo readInfo;
diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/index/UmiIndexer.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/index/UmiIndexer.java
similarity index 81%
rename from src/main/java/com/milaboratory/migec2/core/io/misc/index/UmiIndexer.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/index/UmiIndexer.java
index d4f66cf..6dcd89e 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/misc/index/UmiIndexer.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/index/UmiIndexer.java
@@ -1,12 +1,12 @@
-package com.milaboratory.migec2.core.io.misc.index;
+package com.milaboratory.oncomigec.core.io.misc.index;
 
 import cc.redberry.pipe.Processor;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequencing.read.SequencingRead;
-import com.milaboratory.migec2.core.io.misc.ReadInfo;
-import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult;
-import com.milaboratory.migec2.preproc.demultiplex.processor.CheckoutProcessor;
-import com.milaboratory.migec2.util.ProcessorResultWrapper;
+import com.milaboratory.oncomigec.core.io.misc.ReadInfo;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.CheckoutProcessor;
+import com.milaboratory.oncomigec.util.ProcessorResultWrapper;
 
 public class UmiIndexer implements Processor<SequencingRead, ProcessorResultWrapper<IndexingInfo>> {
     private final CheckoutProcessor checkoutProcessor;
diff --git a/src/main/java/com/milaboratory/migec2/core/io/readers/MigReader.java b/src/main/java/com/milaboratory/oncomigec/core/io/readers/MigReader.java
similarity index 90%
rename from src/main/java/com/milaboratory/migec2/core/io/readers/MigReader.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/readers/MigReader.java
index f89af94..a2bc176 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/readers/MigReader.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/readers/MigReader.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.io.readers;
+package com.milaboratory.oncomigec.core.io.readers;
 
 import cc.redberry.pipe.OutputPort;
 import cc.redberry.pipe.OutputPortCloseable;
@@ -8,16 +8,16 @@
 import cc.redberry.pipe.util.CountingOutputPort;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequencing.read.SequencingRead;
-import com.milaboratory.migec2.core.io.entity.Mig;
-import com.milaboratory.migec2.core.io.misc.MigReaderParameters;
-import com.milaboratory.migec2.core.io.misc.ReadInfo;
-import com.milaboratory.migec2.core.io.misc.UmiHistogram;
-import com.milaboratory.migec2.core.io.misc.index.IndexingInfo;
-import com.milaboratory.migec2.core.io.misc.index.UmiIndexer;
-import com.milaboratory.migec2.pipeline.MigecCli;
-import com.milaboratory.migec2.preproc.demultiplex.processor.CheckoutProcessor;
-import com.milaboratory.migec2.preproc.demultiplex.processor.HeaderParser;
-import com.milaboratory.migec2.util.ProcessorResultWrapper;
+import com.milaboratory.oncomigec.core.io.entity.Mig;
+import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters;
+import com.milaboratory.oncomigec.core.io.misc.ReadInfo;
+import com.milaboratory.oncomigec.core.io.misc.UmiHistogram;
+import com.milaboratory.oncomigec.core.io.misc.index.IndexingInfo;
+import com.milaboratory.oncomigec.core.io.misc.index.UmiIndexer;
+import com.milaboratory.oncomigec.pipeline.MigecCli;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.CheckoutProcessor;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.HeaderParser;
+import com.milaboratory.oncomigec.util.ProcessorResultWrapper;
 
 import java.util.*;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/io/readers/PMigReader.java b/src/main/java/com/milaboratory/oncomigec/core/io/readers/PMigReader.java
similarity index 92%
rename from src/main/java/com/milaboratory/migec2/core/io/readers/PMigReader.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/readers/PMigReader.java
index 78a4630..41b8d61 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/readers/PMigReader.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/readers/PMigReader.java
@@ -13,26 +13,25 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.io.readers;
+package com.milaboratory.oncomigec.core.io.readers;
 
 import cc.redberry.pipe.OutputPortCloseable;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.fastq.PFastqReader;
-import com.milaboratory.core.sequencing.io.fastq.SRandomAccessFastqReader;
 import com.milaboratory.core.sequencing.read.PSequencingRead;
 import com.milaboratory.core.sequencing.read.PSequencingReadImpl;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.core.sequencing.read.SequencingRead;
-import com.milaboratory.migec2.core.io.entity.PMig;
-import com.milaboratory.migec2.core.io.entity.SMig;
-import com.milaboratory.migec2.core.io.misc.MigReaderParameters;
-import com.milaboratory.migec2.core.io.misc.ReadInfo;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult;
-import com.milaboratory.migec2.preproc.demultiplex.entity.PCheckoutResult;
-import com.milaboratory.migec2.preproc.demultiplex.processor.PCheckoutProcessor;
-import com.milaboratory.migec2.preproc.misc.ReadOverlapper;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.core.io.entity.PMig;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
+import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters;
+import com.milaboratory.oncomigec.core.io.misc.ReadInfo;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.PCheckoutResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.PCheckoutProcessor;
+import com.milaboratory.oncomigec.preproc.misc.ReadOverlapper;
+import com.milaboratory.oncomigec.util.Util;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/src/main/java/com/milaboratory/migec2/core/io/readers/SMigReader.java b/src/main/java/com/milaboratory/oncomigec/core/io/readers/SMigReader.java
similarity index 90%
rename from src/main/java/com/milaboratory/migec2/core/io/readers/SMigReader.java
rename to src/main/java/com/milaboratory/oncomigec/core/io/readers/SMigReader.java
index 584b344..aef03f7 100644
--- a/src/main/java/com/milaboratory/migec2/core/io/readers/SMigReader.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/io/readers/SMigReader.java
@@ -13,18 +13,18 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.io.readers;
+package com.milaboratory.oncomigec.core.io.readers;
 
 import cc.redberry.pipe.OutputPortCloseable;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.core.sequencing.read.SequencingRead;
-import com.milaboratory.migec2.core.io.entity.SMig;
-import com.milaboratory.migec2.core.io.misc.MigReaderParameters;
-import com.milaboratory.migec2.core.io.misc.ReadInfo;
-import com.milaboratory.migec2.preproc.demultiplex.processor.SCheckoutProcessor;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
+import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters;
+import com.milaboratory.oncomigec.core.io.misc.ReadInfo;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.SCheckoutProcessor;
+import com.milaboratory.oncomigec.util.Util;
 
 import java.io.File;
 import java.io.IOException;
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/MigecMutation.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutation.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/core/mutations/MigecMutation.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutation.java
index ac556b2..baf9df2 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/MigecMutation.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutation.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.mutations;
+package com.milaboratory.oncomigec.core.mutations;
 
 import com.milaboratory.core.sequence.mutations.MutationType;
 import com.milaboratory.core.sequence.mutations.Mutations;
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/MigecMutationsCollection.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutationsCollection.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/core/mutations/MigecMutationsCollection.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutationsCollection.java
index ff88868..8c8d0c3 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/MigecMutationsCollection.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutationsCollection.java
@@ -1,9 +1,8 @@
-package com.milaboratory.migec2.core.mutations;
+package com.milaboratory.oncomigec.core.mutations;
 
 import com.milaboratory.core.sequence.Range;
 import com.milaboratory.core.sequence.mutations.Mutations;
-import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 import java.util.Iterator;
 import java.util.LinkedList;
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/MutationDifference.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/MutationDifference.java
similarity index 93%
rename from src/main/java/com/milaboratory/migec2/core/mutations/MutationDifference.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/MutationDifference.java
index a84789b..6e1d63d 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/MutationDifference.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/MutationDifference.java
@@ -1,11 +1,9 @@
-package com.milaboratory.migec2.core.mutations;
+package com.milaboratory.oncomigec.core.mutations;
 
 import com.milaboratory.core.sequence.mutations.Mutations;
-import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 import org.apache.commons.collections.iterators.ArrayIterator;
 
-import java.lang.reflect.Array;
 import java.util.Arrays;
 import java.util.Iterator;
 
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/MutationsCollection.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/MutationsCollection.java
similarity index 73%
rename from src/main/java/com/milaboratory/migec2/core/mutations/MutationsCollection.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/MutationsCollection.java
index 239a066..3629f43 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/MutationsCollection.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/MutationsCollection.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.mutations;
+package com.milaboratory.oncomigec.core.mutations;
 
 public interface MutationsCollection {
     public int[] getMutationCodes();
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/DeletionWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/DeletionWrapper.java
similarity index 93%
rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/DeletionWrapper.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/DeletionWrapper.java
index e73b977..ad42019 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/DeletionWrapper.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/DeletionWrapper.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.mutations.wrappers;
+package com.milaboratory.oncomigec.core.mutations.wrappers;
 
 import com.milaboratory.core.sequence.mutations.MutationType;
 import com.milaboratory.core.sequence.mutations.Mutations;
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/IndelWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/IndelWrapper.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/IndelWrapper.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/IndelWrapper.java
index 726e254..e56295f 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/IndelWrapper.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/IndelWrapper.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.mutations.wrappers;
+package com.milaboratory.oncomigec.core.mutations.wrappers;
 
 import com.milaboratory.core.sequence.mutations.MutationType;
 import com.milaboratory.core.sequence.mutations.Mutations;
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/InsertionWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/InsertionWrapper.java
similarity index 92%
rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/InsertionWrapper.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/InsertionWrapper.java
index a0bacae..da5dd21 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/InsertionWrapper.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/InsertionWrapper.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.mutations.wrappers;
+package com.milaboratory.oncomigec.core.mutations.wrappers;
 
 import com.milaboratory.core.sequence.mutations.MutationType;
 import com.milaboratory.core.sequence.mutations.Mutations;
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapper.java
similarity index 90%
rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapper.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapper.java
index 7dfdfcd..9dda03a 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapper.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapper.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.mutations.wrappers;
+package com.milaboratory.oncomigec.core.mutations.wrappers;
 
 import com.milaboratory.core.sequence.mutations.MutationType;
 import com.milaboratory.core.sequence.mutations.Mutations;
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapperCollection.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapperCollection.java
similarity index 92%
rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapperCollection.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapperCollection.java
index 59b2b5a..859b137 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapperCollection.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapperCollection.java
@@ -1,10 +1,9 @@
-package com.milaboratory.migec2.core.mutations.wrappers;
+package com.milaboratory.oncomigec.core.mutations.wrappers;
 
 import com.milaboratory.core.sequence.mutations.MutationType;
 import com.milaboratory.core.sequence.mutations.Mutations;
-import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.mutations.MutationsCollection;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.mutations.MutationsCollection;
 
 import java.util.LinkedList;
 import java.util.List;
diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/SubstitutionWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/SubstitutionWrapper.java
similarity index 94%
rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/SubstitutionWrapper.java
rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/SubstitutionWrapper.java
index 737f4ee..26959ff 100644
--- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/SubstitutionWrapper.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/SubstitutionWrapper.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.mutations.wrappers;
+package com.milaboratory.oncomigec.core.mutations.wrappers;
 
 import com.milaboratory.core.sequence.mutations.MutationType;
 import com.milaboratory.core.sequence.mutations.Mutations;
diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/BaseInstanceFactory.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/BaseInstanceFactory.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/model/classifier/BaseInstanceFactory.java
rename to src/main/java/com/milaboratory/oncomigec/model/classifier/BaseInstanceFactory.java
index 4303262..3522065 100644
--- a/src/main/java/com/milaboratory/migec2/model/classifier/BaseInstanceFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/BaseInstanceFactory.java
@@ -16,9 +16,9 @@
  * Last modified on 25.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.classifier;
+package com.milaboratory.oncomigec.model.classifier;
 
-import com.milaboratory.migec2.model.variant.Variant;
+import com.milaboratory.oncomigec.model.variant.Variant;
 import weka.core.Instance;
 import weka.core.Instances;
 import weka.core.converters.ArffLoader;
diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/BaseVariantClassifier.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/BaseVariantClassifier.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/model/classifier/BaseVariantClassifier.java
rename to src/main/java/com/milaboratory/oncomigec/model/classifier/BaseVariantClassifier.java
index 47a6aab..c64360d 100644
--- a/src/main/java/com/milaboratory/migec2/model/classifier/BaseVariantClassifier.java
+++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/BaseVariantClassifier.java
@@ -16,9 +16,9 @@
  * Last modified on 25.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.classifier;
+package com.milaboratory.oncomigec.model.classifier;
 
-import com.milaboratory.migec2.model.variant.Variant;
+import com.milaboratory.oncomigec.model.variant.Variant;
 import weka.classifiers.Classifier;
 import weka.classifiers.misc.SerializedClassifier;
 import weka.core.Instance;
diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/ClassifierResult.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/ClassifierResult.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/model/classifier/ClassifierResult.java
rename to src/main/java/com/milaboratory/oncomigec/model/classifier/ClassifierResult.java
index 9df90e0..c743241 100644
--- a/src/main/java/com/milaboratory/migec2/model/classifier/ClassifierResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/ClassifierResult.java
@@ -16,7 +16,7 @@
  * Last modified on 23.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.classifier;
+package com.milaboratory.oncomigec.model.classifier;
 
 public class ClassifierResult {
     private final boolean passed;
diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/InstanceFactory.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/InstanceFactory.java
similarity index 91%
rename from src/main/java/com/milaboratory/migec2/model/classifier/InstanceFactory.java
rename to src/main/java/com/milaboratory/oncomigec/model/classifier/InstanceFactory.java
index ce43930..c635cfb 100644
--- a/src/main/java/com/milaboratory/migec2/model/classifier/InstanceFactory.java
+++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/InstanceFactory.java
@@ -16,9 +16,9 @@
  * Last modified on 23.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.classifier;
+package com.milaboratory.oncomigec.model.classifier;
 
-import com.milaboratory.migec2.model.variant.Variant;
+import com.milaboratory.oncomigec.model.variant.Variant;
 import weka.core.Instance;
 import weka.core.Instances;
 
diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/VariantClassifier.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/VariantClassifier.java
similarity index 87%
rename from src/main/java/com/milaboratory/migec2/model/classifier/VariantClassifier.java
rename to src/main/java/com/milaboratory/oncomigec/model/classifier/VariantClassifier.java
index 7292b27..8943663 100644
--- a/src/main/java/com/milaboratory/migec2/model/classifier/VariantClassifier.java
+++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/VariantClassifier.java
@@ -16,9 +16,9 @@
  * Last modified on 26.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.classifier;
+package com.milaboratory.oncomigec.model.classifier;
 
-import com.milaboratory.migec2.model.variant.Variant;
+import com.milaboratory.oncomigec.model.variant.Variant;
 
 public interface VariantClassifier {
     public ClassifierResult classify(Variant variant);
diff --git a/src/main/java/com/milaboratory/migec2/model/variant/Variant.java b/src/main/java/com/milaboratory/oncomigec/model/variant/Variant.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/model/variant/Variant.java
rename to src/main/java/com/milaboratory/oncomigec/model/variant/Variant.java
index a127f81..2097639 100644
--- a/src/main/java/com/milaboratory/migec2/model/variant/Variant.java
+++ b/src/main/java/com/milaboratory/oncomigec/model/variant/Variant.java
@@ -16,10 +16,10 @@
  * Last modified on 20.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.variant;
+package com.milaboratory.oncomigec.model.variant;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 public class Variant {
     private final int pos;
diff --git a/src/main/java/com/milaboratory/migec2/model/variant/VariantContainer.java b/src/main/java/com/milaboratory/oncomigec/model/variant/VariantContainer.java
similarity index 98%
rename from src/main/java/com/milaboratory/migec2/model/variant/VariantContainer.java
rename to src/main/java/com/milaboratory/oncomigec/model/variant/VariantContainer.java
index 1dbdb3a..59e595d 100644
--- a/src/main/java/com/milaboratory/migec2/model/variant/VariantContainer.java
+++ b/src/main/java/com/milaboratory/oncomigec/model/variant/VariantContainer.java
@@ -16,10 +16,10 @@
  * Last modified on 23.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.variant;
+package com.milaboratory.oncomigec.model.variant;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage;
+import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage;
 
 import java.util.Collections;
 import java.util.LinkedList;
diff --git a/src/main/java/com/milaboratory/migec2/model/variant/VariantLibrary.java b/src/main/java/com/milaboratory/oncomigec/model/variant/VariantLibrary.java
similarity index 93%
rename from src/main/java/com/milaboratory/migec2/model/variant/VariantLibrary.java
rename to src/main/java/com/milaboratory/oncomigec/model/variant/VariantLibrary.java
index fff52af..a603f5e 100644
--- a/src/main/java/com/milaboratory/migec2/model/variant/VariantLibrary.java
+++ b/src/main/java/com/milaboratory/oncomigec/model/variant/VariantLibrary.java
@@ -16,11 +16,11 @@
  * Last modified on 1.12.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.variant;
+package com.milaboratory.oncomigec.model.variant;
 
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary;
 
 import java.util.HashMap;
 import java.util.Map;
diff --git a/src/main/java/com/milaboratory/migec2/pipeline/ExomePipeline.java b/src/main/java/com/milaboratory/oncomigec/pipeline/ExomePipeline.java
similarity index 81%
rename from src/main/java/com/milaboratory/migec2/pipeline/ExomePipeline.java
rename to src/main/java/com/milaboratory/oncomigec/pipeline/ExomePipeline.java
index 4cc3659..04b3531 100644
--- a/src/main/java/com/milaboratory/migec2/pipeline/ExomePipeline.java
+++ b/src/main/java/com/milaboratory/oncomigec/pipeline/ExomePipeline.java
@@ -13,23 +13,22 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.pipeline;
+package com.milaboratory.oncomigec.pipeline;
 
-import com.milaboratory.migec2.core.align.processor.AlignerFactoryWithReference;
-import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAlignerFactory;
-import com.milaboratory.migec2.core.align.processor.aligners.SimpleExomeAlignerFactory;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.core.assemble.misc.AssemblerFactory;
-import com.milaboratory.migec2.core.assemble.misc.PAssemblerFactory;
-import com.milaboratory.migec2.core.assemble.misc.SAssemblerFactory;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerFactory;
-import com.milaboratory.migec2.core.consalign.misc.PConsensusAlignerFactory;
-import com.milaboratory.migec2.core.consalign.misc.SConsensusAlignerFactory;
-import com.milaboratory.migec2.core.io.misc.MigReaderParameters;
-import com.milaboratory.migec2.core.io.readers.MigReader;
-import com.milaboratory.migec2.core.io.readers.PMigReader;
-import com.milaboratory.migec2.core.io.readers.SMigReader;
-import com.milaboratory.migec2.preproc.demultiplex.config.BarcodeListParser;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactoryWithReference;
+import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAlignerFactory;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.assemble.misc.AssemblerFactory;
+import com.milaboratory.oncomigec.core.assemble.misc.PAssemblerFactory;
+import com.milaboratory.oncomigec.core.assemble.misc.SAssemblerFactory;
+import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerFactory;
+import com.milaboratory.oncomigec.core.consalign.misc.PConsensusAlignerFactory;
+import com.milaboratory.oncomigec.core.consalign.misc.SConsensusAlignerFactory;
+import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters;
+import com.milaboratory.oncomigec.core.io.readers.MigReader;
+import com.milaboratory.oncomigec.core.io.readers.PMigReader;
+import com.milaboratory.oncomigec.core.io.readers.SMigReader;
+import com.milaboratory.oncomigec.preproc.demultiplex.config.BarcodeListParser;
 import org.apache.commons.io.FileUtils;
 
 import java.io.File;
diff --git a/src/main/java/com/milaboratory/migec2/pipeline/MigecCli.java b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java
similarity index 99%
rename from src/main/java/com/milaboratory/migec2/pipeline/MigecCli.java
rename to src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java
index 90b88cd..398552a 100644
--- a/src/main/java/com/milaboratory/migec2/pipeline/MigecCli.java
+++ b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.pipeline;
+package com.milaboratory.oncomigec.pipeline;
 
-import com.milaboratory.migec2.core.io.misc.MigReaderParameters;
-import com.milaboratory.migec2.core.io.misc.UmiHistogram;
+import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters;
+import com.milaboratory.oncomigec.core.io.misc.UmiHistogram;
 import org.apache.commons.cli.*;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.FilenameUtils;
diff --git a/src/main/java/com/milaboratory/migec2/pipeline/MigecParameterSet.java b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecParameterSet.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/pipeline/MigecParameterSet.java
rename to src/main/java/com/milaboratory/oncomigec/pipeline/MigecParameterSet.java
index 6265f41..27e91f2 100644
--- a/src/main/java/com/milaboratory/migec2/pipeline/MigecParameterSet.java
+++ b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecParameterSet.java
@@ -1,12 +1,12 @@
-package com.milaboratory.migec2.pipeline;
-
-import com.milaboratory.migec2.core.assemble.misc.AssemblerParameters;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters;
-import com.milaboratory.migec2.core.correct.CorrectorParameters;
-import com.milaboratory.migec2.core.haplotype.HaplotypeTreeParameters;
-import com.milaboratory.migec2.preproc.demultiplex.entity.DemultiplexParameters;
-import com.milaboratory.migec2.util.ParameterSet;
-import com.milaboratory.migec2.util.Util;
+package com.milaboratory.oncomigec.pipeline;
+
+import com.milaboratory.oncomigec.core.assemble.misc.AssemblerParameters;
+import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters;
+import com.milaboratory.oncomigec.core.correct.CorrectorParameters;
+import com.milaboratory.oncomigec.core.haplotype.HaplotypeTreeParameters;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.DemultiplexParameters;
+import com.milaboratory.oncomigec.util.ParameterSet;
+import com.milaboratory.oncomigec.util.Util;
 import org.jdom.Document;
 import org.jdom.Element;
 import org.jdom.JDOMException;
diff --git a/src/main/java/com/milaboratory/migec2/pipeline/MigecPipeline.java b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecPipeline.java
similarity index 86%
rename from src/main/java/com/milaboratory/migec2/pipeline/MigecPipeline.java
rename to src/main/java/com/milaboratory/oncomigec/pipeline/MigecPipeline.java
index 99899a3..e9e8e66 100644
--- a/src/main/java/com/milaboratory/migec2/pipeline/MigecPipeline.java
+++ b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecPipeline.java
@@ -1,30 +1,30 @@
-package com.milaboratory.migec2.pipeline;
+package com.milaboratory.oncomigec.pipeline;
 
 import cc.redberry.pipe.OutputPort;
 import cc.redberry.pipe.blocks.Merger;
 import cc.redberry.pipe.blocks.ParallelProcessor;
 import cc.redberry.pipe.util.CountingOutputPort;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.assemble.misc.AssemblerFactory;
-import com.milaboratory.migec2.core.assemble.processor.Assembler;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerFactory;
-import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage;
-import com.milaboratory.migec2.core.consalign.processor.ConsensusAligner;
-import com.milaboratory.migec2.core.correct.CorrectedConsensus;
-import com.milaboratory.migec2.core.correct.Corrector;
-import com.milaboratory.migec2.core.haplotype.HaplotypeTree;
-import com.milaboratory.migec2.core.io.entity.Mig;
-import com.milaboratory.migec2.core.io.misc.UmiHistogram;
-import com.milaboratory.migec2.core.io.readers.MigReader;
-import com.milaboratory.migec2.model.classifier.BaseVariantClassifier;
-import com.milaboratory.migec2.model.classifier.VariantClassifier;
-import com.milaboratory.migec2.model.variant.Variant;
-import com.milaboratory.migec2.model.variant.VariantContainer;
-import com.milaboratory.migec2.model.variant.VariantLibrary;
-import com.milaboratory.migec2.util.ProcessorResultWrapper;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.assemble.misc.AssemblerFactory;
+import com.milaboratory.oncomigec.core.assemble.processor.Assembler;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary;
+import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerFactory;
+import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage;
+import com.milaboratory.oncomigec.core.consalign.processor.ConsensusAligner;
+import com.milaboratory.oncomigec.core.correct.CorrectedConsensus;
+import com.milaboratory.oncomigec.core.correct.Corrector;
+import com.milaboratory.oncomigec.core.haplotype.HaplotypeTree;
+import com.milaboratory.oncomigec.core.io.entity.Mig;
+import com.milaboratory.oncomigec.core.io.misc.UmiHistogram;
+import com.milaboratory.oncomigec.core.io.readers.MigReader;
+import com.milaboratory.oncomigec.model.classifier.BaseVariantClassifier;
+import com.milaboratory.oncomigec.model.classifier.VariantClassifier;
+import com.milaboratory.oncomigec.model.variant.Variant;
+import com.milaboratory.oncomigec.model.variant.VariantContainer;
+import com.milaboratory.oncomigec.model.variant.VariantLibrary;
+import com.milaboratory.oncomigec.util.ProcessorResultWrapper;
 
 import java.util.*;
 
diff --git a/src/main/java/com/milaboratory/migec2/pipeline/TestPipeline.java b/src/main/java/com/milaboratory/oncomigec/pipeline/TestPipeline.java
similarity index 70%
rename from src/main/java/com/milaboratory/migec2/pipeline/TestPipeline.java
rename to src/main/java/com/milaboratory/oncomigec/pipeline/TestPipeline.java
index a3f83cb..255b3f9 100644
--- a/src/main/java/com/milaboratory/migec2/pipeline/TestPipeline.java
+++ b/src/main/java/com/milaboratory/oncomigec/pipeline/TestPipeline.java
@@ -1,12 +1,12 @@
-package com.milaboratory.migec2.pipeline;
-
-import com.milaboratory.migec2.core.io.misc.MigReaderParameters;
-import com.milaboratory.migec2.core.io.readers.PMigReader;
-import com.milaboratory.migec2.core.io.readers.SMigReader;
-import com.milaboratory.migec2.preproc.demultiplex.config.BarcodeListParser;
-import com.milaboratory.migec2.preproc.demultiplex.processor.CheckoutProcessor;
-import com.milaboratory.migec2.preproc.demultiplex.processor.PCheckoutProcessor;
-import com.milaboratory.migec2.preproc.demultiplex.processor.SCheckoutProcessor;
+package com.milaboratory.oncomigec.pipeline;
+
+import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters;
+import com.milaboratory.oncomigec.core.io.readers.PMigReader;
+import com.milaboratory.oncomigec.core.io.readers.SMigReader;
+import com.milaboratory.oncomigec.preproc.demultiplex.config.BarcodeListParser;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.CheckoutProcessor;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.PCheckoutProcessor;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.SCheckoutProcessor;
 import org.apache.commons.io.FileUtils;
 
 import java.io.File;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcher.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java
similarity index 98%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcher.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java
index a3a706b..9e6738f 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcher.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java
@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.barcode;
+package com.milaboratory.oncomigec.preproc.demultiplex.barcode;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.Util;
 
 import java.util.HashSet;
 import java.util.Set;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherResult.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherResult.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherResult.java
index 1485b73..5a2667b 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherResult.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.barcode;
+package com.milaboratory.oncomigec.preproc.demultiplex.barcode;
 
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/config/BarcodeListParser.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/config/BarcodeListParser.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/config/BarcodeListParser.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/config/BarcodeListParser.java
index 6a069b5..f577944 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/config/BarcodeListParser.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/config/BarcodeListParser.java
@@ -13,12 +13,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.config;
+package com.milaboratory.oncomigec.preproc.demultiplex.config;
 
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher;
-import com.milaboratory.migec2.preproc.demultiplex.entity.DemultiplexParameters;
-import com.milaboratory.migec2.preproc.demultiplex.processor.PCheckoutProcessor;
-import com.milaboratory.migec2.preproc.demultiplex.processor.SCheckoutProcessor;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.DemultiplexParameters;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.PCheckoutProcessor;
+import com.milaboratory.oncomigec.preproc.demultiplex.processor.SCheckoutProcessor;
 
 import java.util.ArrayList;
 import java.util.HashSet;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/CheckoutResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/CheckoutResult.java
similarity index 92%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/CheckoutResult.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/CheckoutResult.java
index aea547a..5624e0c 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/CheckoutResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/CheckoutResult.java
@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.entity;
+package com.milaboratory.oncomigec.preproc.demultiplex.entity;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult;
 
 public class CheckoutResult {
     protected final int sampleId;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/DemultiplexParameters.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/DemultiplexParameters.java
similarity index 96%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/DemultiplexParameters.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/DemultiplexParameters.java
index 56c01f4..6297faa 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/DemultiplexParameters.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/DemultiplexParameters.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.preproc.demultiplex.entity;
+package com.milaboratory.oncomigec.preproc.demultiplex.entity;
 
-import com.milaboratory.migec2.util.ParameterSet;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.ParameterSet;
+import com.milaboratory.oncomigec.util.Util;
 import org.jdom.Element;
 
 public class DemultiplexParameters implements ParameterSet{
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/PCheckoutResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/PCheckoutResult.java
similarity index 92%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/PCheckoutResult.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/PCheckoutResult.java
index d993213..39974ff 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/PCheckoutResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/PCheckoutResult.java
@@ -13,10 +13,10 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.entity;
+package com.milaboratory.oncomigec.preproc.demultiplex.entity;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult;
 
 public final class PCheckoutResult extends CheckoutResult {
     private final boolean masterFirst;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SCheckoutResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SCheckoutResult.java
similarity index 62%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SCheckoutResult.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SCheckoutResult.java
index 57b1f9c..4c4c71a 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SCheckoutResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SCheckoutResult.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.preproc.demultiplex.entity;
+package com.milaboratory.oncomigec.preproc.demultiplex.entity;
 
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult;
 
 public final class SCheckoutResult extends CheckoutResult {
     public SCheckoutResult(int sampleId, String sampleName, boolean foundInRC, BarcodeSearcherResult masterResult) {
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SimpleCheckoutResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SimpleCheckoutResult.java
similarity index 72%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SimpleCheckoutResult.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SimpleCheckoutResult.java
index 315a99f..8d6e4bd 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SimpleCheckoutResult.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SimpleCheckoutResult.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.preproc.demultiplex.entity;
+package com.milaboratory.oncomigec.preproc.demultiplex.entity;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult;
 
 public final class SimpleCheckoutResult extends CheckoutResult {
     public SimpleCheckoutResult(String sampleName, NucleotideSQPair umiSQPair) {
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessor.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessor.java
similarity index 94%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessor.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessor.java
index 1cad24d..76937c5 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessor.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessor.java
@@ -13,11 +13,11 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.processor;
+package com.milaboratory.oncomigec.preproc.demultiplex.processor;
 
 import com.milaboratory.core.sequencing.read.SequencingRead;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher;
-import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/HeaderParser.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/HeaderParser.java
similarity index 72%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/HeaderParser.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/HeaderParser.java
index cd5538e..2fce8d9 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/HeaderParser.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/HeaderParser.java
@@ -1,11 +1,11 @@
-package com.milaboratory.migec2.preproc.demultiplex.processor;
+package com.milaboratory.oncomigec.preproc.demultiplex.processor;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequencing.read.SequencingRead;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher;
-import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult;
-import com.milaboratory.migec2.preproc.demultiplex.entity.SimpleCheckoutResult;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.SimpleCheckoutResult;
+import com.milaboratory.oncomigec.util.Util;
 
 public final class HeaderParser extends CheckoutProcessor<CheckoutResult, SequencingRead> {
     private final String sampleName;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/PCheckoutProcessor.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/PCheckoutProcessor.java
similarity index 95%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/PCheckoutProcessor.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/PCheckoutProcessor.java
index 2e225cf..2168437 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/PCheckoutProcessor.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/PCheckoutProcessor.java
@@ -13,13 +13,13 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.processor;
+package com.milaboratory.oncomigec.preproc.demultiplex.processor;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequencing.read.PSequencingRead;
-import com.milaboratory.migec2.preproc.demultiplex.entity.PCheckoutResult;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.PCheckoutResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult;
 
 import java.util.List;
 import java.util.concurrent.atomic.AtomicLong;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/ReadPositionUmiExtractor.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/ReadPositionUmiExtractor.java
similarity index 81%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/ReadPositionUmiExtractor.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/ReadPositionUmiExtractor.java
index fb07223..705699f 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/ReadPositionUmiExtractor.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/ReadPositionUmiExtractor.java
@@ -14,14 +14,14 @@
  * limitations under the License.
  */
 
-package com.milaboratory.migec2.preproc.demultiplex.processor;
+package com.milaboratory.oncomigec.preproc.demultiplex.processor;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequencing.read.SequencingRead;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher;
-import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult;
-import com.milaboratory.migec2.preproc.demultiplex.entity.SimpleCheckoutResult;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.SimpleCheckoutResult;
+import com.milaboratory.oncomigec.util.Util;
 
 public class ReadPositionUmiExtractor extends CheckoutProcessor<CheckoutResult, SequencingRead> {
     private final String sampleName;
diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/SCheckoutProcessor.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/SCheckoutProcessor.java
similarity index 85%
rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/SCheckoutProcessor.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/SCheckoutProcessor.java
index 7569c06..df8a0de 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/SCheckoutProcessor.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/SCheckoutProcessor.java
@@ -13,14 +13,12 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.processor;
+package com.milaboratory.oncomigec.preproc.demultiplex.processor;
 
 import com.milaboratory.core.sequencing.read.SSequencingRead;
-import com.milaboratory.migec2.preproc.demultiplex.entity.SCheckoutResult;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher;
-import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult;
-
-import java.util.Arrays;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.SCheckoutResult;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher;
+import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult;
 
 public final class SCheckoutProcessor extends CheckoutProcessor<SCheckoutResult, SSequencingRead> {
     public SCheckoutProcessor(String[] sampleNames, BarcodeSearcher[] masterBarcodes) {
diff --git a/src/main/java/com/milaboratory/migec2/preproc/misc/ReadOverlapper.java b/src/main/java/com/milaboratory/oncomigec/preproc/misc/ReadOverlapper.java
similarity index 99%
rename from src/main/java/com/milaboratory/migec2/preproc/misc/ReadOverlapper.java
rename to src/main/java/com/milaboratory/oncomigec/preproc/misc/ReadOverlapper.java
index 97b0a89..ec74028 100644
--- a/src/main/java/com/milaboratory/migec2/preproc/misc/ReadOverlapper.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/misc/ReadOverlapper.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.misc;
+package com.milaboratory.oncomigec.preproc.misc;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequencing.read.PSequencingRead;
diff --git a/src/main/java/com/milaboratory/migec2/util/Basics.java b/src/main/java/com/milaboratory/oncomigec/util/Basics.java
similarity index 99%
rename from src/main/java/com/milaboratory/migec2/util/Basics.java
rename to src/main/java/com/milaboratory/oncomigec/util/Basics.java
index 112c9eb..029d29f 100644
--- a/src/main/java/com/milaboratory/migec2/util/Basics.java
+++ b/src/main/java/com/milaboratory/oncomigec/util/Basics.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.util;
+package com.milaboratory.oncomigec.util;
 
 import org.jdom.Document;
 import org.jdom.Element;
diff --git a/src/main/java/com/milaboratory/migec2/util/ParameterSet.java b/src/main/java/com/milaboratory/oncomigec/util/ParameterSet.java
similarity index 68%
rename from src/main/java/com/milaboratory/migec2/util/ParameterSet.java
rename to src/main/java/com/milaboratory/oncomigec/util/ParameterSet.java
index 6f1570a..25f7942 100644
--- a/src/main/java/com/milaboratory/migec2/util/ParameterSet.java
+++ b/src/main/java/com/milaboratory/oncomigec/util/ParameterSet.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.util;
+package com.milaboratory.oncomigec.util;
 
 import org.jdom.Element;
 
diff --git a/src/main/java/com/milaboratory/migec2/util/ProcessorResultWrapper.java b/src/main/java/com/milaboratory/oncomigec/util/ProcessorResultWrapper.java
similarity index 92%
rename from src/main/java/com/milaboratory/migec2/util/ProcessorResultWrapper.java
rename to src/main/java/com/milaboratory/oncomigec/util/ProcessorResultWrapper.java
index b61722e..96e466f 100644
--- a/src/main/java/com/milaboratory/migec2/util/ProcessorResultWrapper.java
+++ b/src/main/java/com/milaboratory/oncomigec/util/ProcessorResultWrapper.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.util;
+package com.milaboratory.oncomigec.util;
 
 public class ProcessorResultWrapper<T> {
     private final T result;
diff --git a/src/main/java/com/milaboratory/migec2/util/QualityHistogram.java b/src/main/java/com/milaboratory/oncomigec/util/QualityHistogram.java
similarity index 97%
rename from src/main/java/com/milaboratory/migec2/util/QualityHistogram.java
rename to src/main/java/com/milaboratory/oncomigec/util/QualityHistogram.java
index 569fee3..9e593b3 100644
--- a/src/main/java/com/milaboratory/migec2/util/QualityHistogram.java
+++ b/src/main/java/com/milaboratory/oncomigec/util/QualityHistogram.java
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package com.milaboratory.migec2.util;
+package com.milaboratory.oncomigec.util;
 
 import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
 
diff --git a/src/main/java/com/milaboratory/migec2/util/Util.java b/src/main/java/com/milaboratory/oncomigec/util/Util.java
similarity index 99%
rename from src/main/java/com/milaboratory/migec2/util/Util.java
rename to src/main/java/com/milaboratory/oncomigec/util/Util.java
index c164c5f..cbf9924 100644
--- a/src/main/java/com/milaboratory/migec2/util/Util.java
+++ b/src/main/java/com/milaboratory/oncomigec/util/Util.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.util;
+package com.milaboratory.oncomigec.util;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.SequenceBuilder;
diff --git a/src/test/java/com/milaboratory/migec2/core/align/kmer/KMerFinderTest.java b/src/test/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderTest.java
similarity index 87%
rename from src/test/java/com/milaboratory/migec2/core/align/kmer/KMerFinderTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderTest.java
index 40aacf0..193fe88 100644
--- a/src/test/java/com/milaboratory/migec2/core/align/kmer/KMerFinderTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderTest.java
@@ -1,11 +1,10 @@
-package com.milaboratory.migec2.core.align.kmer;
+package com.milaboratory.oncomigec.core.align.kmer;
 
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.util.testing.IntRange;
-import com.milaboratory.migec2.util.testing.PercentRange;
-import com.milaboratory.migec2.util.testing.generators.GeneratorMutationModel;
-import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator;
-import org.junit.Test;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.util.testing.IntRange;
+import com.milaboratory.oncomigec.util.testing.PercentRange;
+import com.milaboratory.oncomigec.util.testing.generators.GeneratorMutationModel;
+import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator;
 
 import java.util.Arrays;
 
diff --git a/src/test/java/com/milaboratory/migec2/core/align/processor/aligners/AlignersTest.java b/src/test/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignersTest.java
similarity index 91%
rename from src/test/java/com/milaboratory/migec2/core/align/processor/aligners/AlignersTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignersTest.java
index 8a09258..8e1cdd0 100644
--- a/src/test/java/com/milaboratory/migec2/core/align/processor/aligners/AlignersTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignersTest.java
@@ -13,16 +13,16 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.align.processor.aligners;
+package com.milaboratory.oncomigec.core.align.processor.aligners;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.processor.Aligner;
-import com.milaboratory.migec2.core.align.processor.AlignerFactory;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.util.testing.PercentRange;
-import com.milaboratory.migec2.util.testing.generators.RandomIndelGenerator;
-import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.processor.Aligner;
+import com.milaboratory.oncomigec.core.align.processor.AlignerFactory;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.util.testing.PercentRange;
+import com.milaboratory.oncomigec.util.testing.generators.RandomIndelGenerator;
+import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator;
 import org.junit.Test;
 
 import java.io.IOException;
diff --git a/src/test/java/com/milaboratory/migec2/core/assemble/processor/AssemblerTest.java b/src/test/java/com/milaboratory/oncomigec/core/assemble/processor/AssemblerTest.java
similarity index 92%
rename from src/test/java/com/milaboratory/migec2/core/assemble/processor/AssemblerTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/assemble/processor/AssemblerTest.java
index 75adbb8..4e38380 100644
--- a/src/test/java/com/milaboratory/migec2/core/assemble/processor/AssemblerTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/assemble/processor/AssemblerTest.java
@@ -13,24 +13,24 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.assemble.processor;
+package com.milaboratory.oncomigec.core.assemble.processor;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.io.entity.Mig;
-import com.milaboratory.migec2.core.io.entity.SMig;
-import com.milaboratory.migec2.util.Basics;
-import com.milaboratory.migec2.util.testing.generators.RandomMigGenerator;
-import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.io.entity.Mig;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
+import com.milaboratory.oncomigec.util.Basics;
+import com.milaboratory.oncomigec.util.testing.generators.RandomMigGenerator;
+import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator;
 import org.junit.Assert;
 import org.junit.Test;
 
 import java.util.ArrayList;
 import java.util.List;
 
-import static com.milaboratory.migec2.util.Util.*;
+import static com.milaboratory.oncomigec.util.Util.*;
 
 public class AssemblerTest {
     private static final int nRepetitions = 1000, randomTestAssertThreshold = 70, randomTestAssertIDHThreshold = 60;
diff --git a/src/test/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractorTest.java b/src/test/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractorTest.java
similarity index 95%
rename from src/test/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractorTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractorTest.java
index 6ba6deb..c61f150 100644
--- a/src/test/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractorTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractorTest.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.core.consalign.mutations;
+package com.milaboratory.oncomigec.core.consalign.mutations;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.alignment.KAligner;
@@ -8,17 +8,17 @@
 import com.milaboratory.core.sequence.mutations.MutationType;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet;
-import com.milaboratory.migec2.core.align.entity.SAlignmentResult;
-import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAligner;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.assemble.processor.SAssembler;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters;
-import com.milaboratory.migec2.core.io.entity.SMig;
-import com.milaboratory.migec2.util.Basics;
-import com.milaboratory.migec2.util.testing.generators.GeneratorMutationModel;
-import com.milaboratory.migec2.util.testing.generators.RandomMigGenerator;
-import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator;
+import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult;
+import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAligner;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.assemble.processor.SAssembler;
+import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
+import com.milaboratory.oncomigec.util.Basics;
+import com.milaboratory.oncomigec.util.testing.generators.GeneratorMutationModel;
+import com.milaboratory.oncomigec.util.testing.generators.RandomMigGenerator;
+import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator;
 import org.junit.Assert;
 import org.junit.Test;
 
diff --git a/src/test/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAlignerTest.java b/src/test/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAlignerTest.java
similarity index 85%
rename from src/test/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAlignerTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAlignerTest.java
index 8f01621..239ccc9 100644
--- a/src/test/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAlignerTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAlignerTest.java
@@ -13,24 +13,24 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.consalign.processor;
-
-import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAligner;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.assemble.misc.AssemblerParameters;
-import com.milaboratory.migec2.core.assemble.processor.Assembler;
-import com.milaboratory.migec2.core.assemble.processor.SAssembler;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage;
-import com.milaboratory.migec2.core.io.entity.SMig;
-import com.milaboratory.migec2.util.Basics;
-import com.milaboratory.migec2.util.testing.DoubleRange;
-import com.milaboratory.migec2.util.testing.PercentRange;
-import com.milaboratory.migec2.util.testing.generators.GeneratorMutationModel;
-import com.milaboratory.migec2.util.testing.generators.RandomMigGenerator;
-import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator;
+package com.milaboratory.oncomigec.core.consalign.processor;
+
+import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAligner;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.assemble.misc.AssemblerParameters;
+import com.milaboratory.oncomigec.core.assemble.processor.Assembler;
+import com.milaboratory.oncomigec.core.assemble.processor.SAssembler;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
+import com.milaboratory.oncomigec.util.Basics;
+import com.milaboratory.oncomigec.util.testing.DoubleRange;
+import com.milaboratory.oncomigec.util.testing.PercentRange;
+import com.milaboratory.oncomigec.util.testing.generators.GeneratorMutationModel;
+import com.milaboratory.oncomigec.util.testing.generators.RandomMigGenerator;
+import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator;
 import org.junit.Test;
 
 import java.util.Arrays;
diff --git a/src/test/java/com/milaboratory/migec2/core/correct/CorrectorTest.java b/src/test/java/com/milaboratory/oncomigec/core/correct/CorrectorTest.java
similarity index 82%
rename from src/test/java/com/milaboratory/migec2/core/correct/CorrectorTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/correct/CorrectorTest.java
index b8503f7..e2a17f9 100644
--- a/src/test/java/com/milaboratory/migec2/core/correct/CorrectorTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/correct/CorrectorTest.java
@@ -13,21 +13,20 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.correct;
+package com.milaboratory.oncomigec.core.correct;
 
-import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAligner;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.core.assemble.entity.SConsensus;
-import com.milaboratory.migec2.core.assemble.processor.SAssembler;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters;
-import com.milaboratory.migec2.core.consalign.processor.ConsensusAligner;
-import com.milaboratory.migec2.core.consalign.processor.SConsensusAligner;
-import com.milaboratory.migec2.core.io.entity.SMig;
-import com.milaboratory.migec2.util.testing.generators.GeneratorMutationModel;
-import com.milaboratory.migec2.util.testing.generators.RandomMigGenerator;
-import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator;
+import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAligner;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.assemble.entity.SConsensus;
+import com.milaboratory.oncomigec.core.assemble.processor.SAssembler;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.consalign.processor.ConsensusAligner;
+import com.milaboratory.oncomigec.core.consalign.processor.SConsensusAligner;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
+import com.milaboratory.oncomigec.util.testing.generators.GeneratorMutationModel;
+import com.milaboratory.oncomigec.util.testing.generators.RandomMigGenerator;
+import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator;
 import org.junit.Assert;
 import org.junit.Test;
 
diff --git a/src/test/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeDataTest.java b/src/test/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeDataTest.java
similarity index 85%
rename from src/test/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeDataTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeDataTest.java
index 51c6968..a68bf77 100644
--- a/src/test/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeDataTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeDataTest.java
@@ -13,22 +13,22 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.haplotype;
+package com.milaboratory.oncomigec.core.haplotype;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAligner;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
-import com.milaboratory.migec2.core.assemble.entity.Consensus;
-import com.milaboratory.migec2.core.assemble.processor.Assembler;
-import com.milaboratory.migec2.core.assemble.processor.PAssembler;
-import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus;
-import com.milaboratory.migec2.core.consalign.processor.ConsensusAligner;
-import com.milaboratory.migec2.core.consalign.processor.PConsensusAligner;
-import com.milaboratory.migec2.core.correct.CorrectedConsensus;
-import com.milaboratory.migec2.core.correct.Corrector;
-import com.milaboratory.migec2.core.io.entity.PMig;
-import com.milaboratory.migec2.core.io.readers.PMigReader;
-import com.milaboratory.migec2.util.testing.TestResources;
+import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAligner;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.assemble.entity.Consensus;
+import com.milaboratory.oncomigec.core.assemble.processor.Assembler;
+import com.milaboratory.oncomigec.core.assemble.processor.PAssembler;
+import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus;
+import com.milaboratory.oncomigec.core.consalign.processor.ConsensusAligner;
+import com.milaboratory.oncomigec.core.consalign.processor.PConsensusAligner;
+import com.milaboratory.oncomigec.core.correct.CorrectedConsensus;
+import com.milaboratory.oncomigec.core.correct.Corrector;
+import com.milaboratory.oncomigec.core.io.entity.PMig;
+import com.milaboratory.oncomigec.core.io.readers.PMigReader;
+import com.milaboratory.oncomigec.util.testing.TestResources;
 import org.junit.Assert;
 
 import java.util.ArrayList;
diff --git a/src/test/java/com/milaboratory/migec2/core/io/misc/UmiHistogramTest.java b/src/test/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogramTest.java
similarity index 94%
rename from src/test/java/com/milaboratory/migec2/core/io/misc/UmiHistogramTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogramTest.java
index ca131ed..95e98af 100644
--- a/src/test/java/com/milaboratory/migec2/core/io/misc/UmiHistogramTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogramTest.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.core.io.misc;
+package com.milaboratory.oncomigec.core.io.misc;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.Util;
 import org.apache.commons.math.random.MersenneTwister;
 import org.apache.commons.math.random.RandomGenerator;
 import org.junit.Assert;
diff --git a/src/test/java/com/milaboratory/migec2/core/io/readers/PMigReaderTest.java b/src/test/java/com/milaboratory/oncomigec/core/io/readers/PMigReaderTest.java
similarity index 91%
rename from src/test/java/com/milaboratory/migec2/core/io/readers/PMigReaderTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/io/readers/PMigReaderTest.java
index 6f4502d..bc6e2ed 100644
--- a/src/test/java/com/milaboratory/migec2/core/io/readers/PMigReaderTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/io/readers/PMigReaderTest.java
@@ -13,19 +13,18 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.io.readers;
+package com.milaboratory.oncomigec.core.io.readers;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
-import com.milaboratory.migec2.core.io.entity.PMig;
-import com.milaboratory.migec2.core.io.misc.MigReaderParameters;
-import com.milaboratory.migec2.core.io.misc.UmiHistogram;
-import com.milaboratory.migec2.preproc.demultiplex.config.BarcodeListParser;
-import com.milaboratory.migec2.util.testing.TestResources;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.core.io.entity.PMig;
+import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters;
+import com.milaboratory.oncomigec.core.io.misc.UmiHistogram;
+import com.milaboratory.oncomigec.preproc.demultiplex.config.BarcodeListParser;
+import com.milaboratory.oncomigec.util.testing.TestResources;
+import com.milaboratory.oncomigec.util.Util;
 import org.junit.Assert;
-import org.junit.Test;
 
 import java.io.File;
 import java.util.ArrayList;
diff --git a/src/test/java/com/milaboratory/migec2/core/io/readers/SMigReaderTest.java b/src/test/java/com/milaboratory/oncomigec/core/io/readers/SMigReaderTest.java
similarity index 86%
rename from src/test/java/com/milaboratory/migec2/core/io/readers/SMigReaderTest.java
rename to src/test/java/com/milaboratory/oncomigec/core/io/readers/SMigReaderTest.java
index cfb2617..811680f 100644
--- a/src/test/java/com/milaboratory/migec2/core/io/readers/SMigReaderTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/core/io/readers/SMigReaderTest.java
@@ -13,16 +13,15 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.core.io.readers;
+package com.milaboratory.oncomigec.core.io.readers;
 
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
-import com.milaboratory.migec2.core.io.entity.SMig;
-import com.milaboratory.migec2.core.io.misc.MigReaderParameters;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
+import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters;
 import org.junit.Assert;
-import org.junit.Test;
-import com.milaboratory.migec2.util.testing.TestResources;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.testing.TestResources;
+import com.milaboratory.oncomigec.util.Util;
 
 import java.io.File;
 
diff --git a/src/test/java/com/milaboratory/migec2/model/classifier/ClassifierTest.java b/src/test/java/com/milaboratory/oncomigec/model/classifier/ClassifierTest.java
similarity index 94%
rename from src/test/java/com/milaboratory/migec2/model/classifier/ClassifierTest.java
rename to src/test/java/com/milaboratory/oncomigec/model/classifier/ClassifierTest.java
index 0d7eb1e..4092d68 100644
--- a/src/test/java/com/milaboratory/migec2/model/classifier/ClassifierTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/model/classifier/ClassifierTest.java
@@ -16,7 +16,7 @@
  * Last modified on 27.11.2014 by mikesh
  */
 
-package com.milaboratory.migec2.model.classifier;
+package com.milaboratory.oncomigec.model.classifier;
 
 import org.junit.Assert;
 import org.junit.Test;
diff --git a/src/test/java/com/milaboratory/migec2/pipeline/MigecParameterSetTest.java b/src/test/java/com/milaboratory/oncomigec/pipeline/MigecParameterSetTest.java
similarity index 91%
rename from src/test/java/com/milaboratory/migec2/pipeline/MigecParameterSetTest.java
rename to src/test/java/com/milaboratory/oncomigec/pipeline/MigecParameterSetTest.java
index 1677ee3..06f1ce0 100644
--- a/src/test/java/com/milaboratory/migec2/pipeline/MigecParameterSetTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/pipeline/MigecParameterSetTest.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.pipeline;
+package com.milaboratory.oncomigec.pipeline;
 
-import com.milaboratory.migec2.util.Basics;
+import com.milaboratory.oncomigec.util.Basics;
 import org.jdom.Element;
 import org.jdom.JDOMException;
 import org.junit.Assert;
@@ -8,7 +8,6 @@
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
-import java.io.File;
 import java.io.IOException;
 
 public class MigecParameterSetTest {
diff --git a/src/test/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherTest.java b/src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherTest.java
similarity index 98%
rename from src/test/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherTest.java
rename to src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherTest.java
index 9cf4134..417f687 100644
--- a/src/test/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherTest.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.barcode;
+package com.milaboratory.oncomigec.preproc.demultiplex.barcode;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.mutations.GenericNucleotideMutationModel;
@@ -24,8 +24,8 @@
 import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
 import com.milaboratory.core.sequencing.io.fastq.SFastqReader;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
-import com.milaboratory.migec2.util.testing.TestResources;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.testing.TestResources;
+import com.milaboratory.oncomigec.util.Util;
 import org.junit.Assert;
 import org.junit.Test;
 
diff --git a/src/test/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessorTest.java b/src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessorTest.java
similarity index 87%
rename from src/test/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessorTest.java
rename to src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessorTest.java
index 7b02df8..82b4599 100644
--- a/src/test/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessorTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessorTest.java
@@ -13,19 +13,18 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.demultiplex.processor;
+package com.milaboratory.oncomigec.preproc.demultiplex.processor;
 
 import com.milaboratory.core.sequence.quality.QualityFormat;
 import com.milaboratory.core.sequencing.io.fastq.PFastqReader;
 import com.milaboratory.core.sequencing.read.PSequencingRead;
-import com.milaboratory.migec2.preproc.demultiplex.config.BarcodeListParser;
-import com.milaboratory.migec2.preproc.demultiplex.entity.DemultiplexParameters;
-import com.milaboratory.migec2.util.testing.TestResources;
+import com.milaboratory.oncomigec.preproc.demultiplex.config.BarcodeListParser;
+import com.milaboratory.oncomigec.preproc.demultiplex.entity.DemultiplexParameters;
+import com.milaboratory.oncomigec.util.testing.TestResources;
 import com.milaboratory.util.CompressionType;
 import org.apache.commons.io.FileUtils;
 import org.junit.Assert;
 import org.junit.Rule;
-import org.junit.Test;
 import org.junit.rules.ExpectedException;
 
 import java.util.List;
diff --git a/src/test/java/com/milaboratory/migec2/preproc/misc/OverlapTest.java b/src/test/java/com/milaboratory/oncomigec/preproc/misc/OverlapTest.java
similarity index 98%
rename from src/test/java/com/milaboratory/migec2/preproc/misc/OverlapTest.java
rename to src/test/java/com/milaboratory/oncomigec/preproc/misc/OverlapTest.java
index 6dc0062..6ed7d85 100644
--- a/src/test/java/com/milaboratory/migec2/preproc/misc/OverlapTest.java
+++ b/src/test/java/com/milaboratory/oncomigec/preproc/misc/OverlapTest.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.preproc.misc;
+package com.milaboratory.oncomigec.preproc.misc;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.mutations.MutationModels;
@@ -31,7 +31,7 @@
 
 import java.util.Arrays;
 
-import static com.milaboratory.migec2.util.Util.randomSequence;
+import static com.milaboratory.oncomigec.util.Util.randomSequence;
 
 
 public class OverlapTest {
diff --git a/src/test/java/com/milaboratory/migec2/util/testing/DoubleRange.java b/src/test/java/com/milaboratory/oncomigec/util/testing/DoubleRange.java
similarity index 97%
rename from src/test/java/com/milaboratory/migec2/util/testing/DoubleRange.java
rename to src/test/java/com/milaboratory/oncomigec/util/testing/DoubleRange.java
index 31800c1..45c5998 100644
--- a/src/test/java/com/milaboratory/migec2/util/testing/DoubleRange.java
+++ b/src/test/java/com/milaboratory/oncomigec/util/testing/DoubleRange.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.util.testing;
+package com.milaboratory.oncomigec.util.testing;
 
 import org.junit.Assert;
 
diff --git a/src/test/java/com/milaboratory/migec2/util/testing/IntRange.java b/src/test/java/com/milaboratory/oncomigec/util/testing/IntRange.java
similarity index 97%
rename from src/test/java/com/milaboratory/migec2/util/testing/IntRange.java
rename to src/test/java/com/milaboratory/oncomigec/util/testing/IntRange.java
index 40f1857..9619cb2 100644
--- a/src/test/java/com/milaboratory/migec2/util/testing/IntRange.java
+++ b/src/test/java/com/milaboratory/oncomigec/util/testing/IntRange.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.util.testing;
+package com.milaboratory.oncomigec.util.testing;
 
 import org.junit.Assert;
 
diff --git a/src/test/java/com/milaboratory/migec2/util/testing/PercentRange.java b/src/test/java/com/milaboratory/oncomigec/util/testing/PercentRange.java
similarity index 95%
rename from src/test/java/com/milaboratory/migec2/util/testing/PercentRange.java
rename to src/test/java/com/milaboratory/oncomigec/util/testing/PercentRange.java
index abf87ca..caa0f65 100644
--- a/src/test/java/com/milaboratory/migec2/util/testing/PercentRange.java
+++ b/src/test/java/com/milaboratory/oncomigec/util/testing/PercentRange.java
@@ -1,6 +1,6 @@
-package com.milaboratory.migec2.util.testing;
+package com.milaboratory.oncomigec.util.testing;
 
-import com.milaboratory.migec2.util.Basics;
+import com.milaboratory.oncomigec.util.Basics;
 import org.junit.Assert;
 
 public class PercentRange {
diff --git a/src/test/java/com/milaboratory/migec2/util/testing/TestResources.java b/src/test/java/com/milaboratory/oncomigec/util/testing/TestResources.java
similarity index 95%
rename from src/test/java/com/milaboratory/migec2/util/testing/TestResources.java
rename to src/test/java/com/milaboratory/oncomigec/util/testing/TestResources.java
index 5e590cc..6cd1d60 100644
--- a/src/test/java/com/milaboratory/migec2/util/testing/TestResources.java
+++ b/src/test/java/com/milaboratory/oncomigec/util/testing/TestResources.java
@@ -13,7 +13,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package com.milaboratory.migec2.util.testing;
+package com.milaboratory.oncomigec.util.testing;
 
 import org.junit.Assume;
 
diff --git a/src/test/java/com/milaboratory/migec2/util/testing/generators/GeneratorMutationModel.java b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/GeneratorMutationModel.java
similarity index 95%
rename from src/test/java/com/milaboratory/migec2/util/testing/generators/GeneratorMutationModel.java
rename to src/test/java/com/milaboratory/oncomigec/util/testing/generators/GeneratorMutationModel.java
index 8e10579..88d4039 100644
--- a/src/test/java/com/milaboratory/migec2/util/testing/generators/GeneratorMutationModel.java
+++ b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/GeneratorMutationModel.java
@@ -1,11 +1,11 @@
-package com.milaboratory.migec2.util.testing.generators;
+package com.milaboratory.oncomigec.util.testing.generators;
 
 import com.milaboratory.core.sequence.mutations.GenericNucleotideMutationModel;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.mutations.NucleotideMutationModel;
 import com.milaboratory.core.sequence.mutations.SubstitutionModels;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
 
 import java.util.Random;
 
diff --git a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomIndelGenerator.java b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomIndelGenerator.java
similarity index 92%
rename from src/test/java/com/milaboratory/migec2/util/testing/generators/RandomIndelGenerator.java
rename to src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomIndelGenerator.java
index 68527f9..3950697 100644
--- a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomIndelGenerator.java
+++ b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomIndelGenerator.java
@@ -1,7 +1,7 @@
-package com.milaboratory.migec2.util.testing.generators;
+package com.milaboratory.oncomigec.util.testing.generators;
 
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
-import com.milaboratory.migec2.util.Util;
+import com.milaboratory.oncomigec.util.Util;
 
 public class RandomIndelGenerator {
     private final int minIndelSize, maxIndelSize;
diff --git a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomMigGenerator.java b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomMigGenerator.java
similarity index 95%
rename from src/test/java/com/milaboratory/migec2/util/testing/generators/RandomMigGenerator.java
rename to src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomMigGenerator.java
index 81b64cb..c201312 100644
--- a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomMigGenerator.java
+++ b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomMigGenerator.java
@@ -1,4 +1,4 @@
-package com.milaboratory.migec2.util.testing.generators;
+package com.milaboratory.oncomigec.util.testing.generators;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.mutations.Mutations;
@@ -6,12 +6,12 @@
 import com.milaboratory.core.sequence.quality.SequenceQualityPhred;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.core.sequencing.read.SSequencingReadImpl;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.io.entity.SMig;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.io.entity.SMig;
 
 import java.util.*;
 
-import static com.milaboratory.migec2.util.Util.randomSequence;
+import static com.milaboratory.oncomigec.util.Util.randomSequence;
 
 public class RandomMigGenerator {
     private int migSizeMin, migSizeMax;
diff --git a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomReferenceGenerator.java b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomReferenceGenerator.java
similarity index 95%
rename from src/test/java/com/milaboratory/migec2/util/testing/generators/RandomReferenceGenerator.java
rename to src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomReferenceGenerator.java
index 806dc2d..b1b92ba 100644
--- a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomReferenceGenerator.java
+++ b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomReferenceGenerator.java
@@ -1,12 +1,12 @@
-package com.milaboratory.migec2.util.testing.generators;
+package com.milaboratory.oncomigec.util.testing.generators;
 
 import com.milaboratory.core.sequence.NucleotideSQPair;
 import com.milaboratory.core.sequence.mutations.Mutations;
 import com.milaboratory.core.sequence.nucleotide.NucleotideSequence;
 import com.milaboratory.core.sequencing.read.SSequencingRead;
 import com.milaboratory.core.sequencing.read.SSequencingReadImpl;
-import com.milaboratory.migec2.core.align.reference.Reference;
-import com.milaboratory.migec2.core.align.reference.ReferenceLibrary;
+import com.milaboratory.oncomigec.core.align.reference.Reference;
+import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary;
 
 import java.util.HashSet;
 import java.util.LinkedList;
@@ -14,7 +14,7 @@
 import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import static com.milaboratory.migec2.util.Util.randomSequence;
+import static com.milaboratory.oncomigec.util.Util.randomSequence;
 
 public class RandomReferenceGenerator {
     private int referenceSizeMin, referenceSizeMax;