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dhusondhuson
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purging CE
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‎README.md

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@@ -12,7 +12,7 @@ A key novel feature of the SplitsTree App is that all data, algorithms and param
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Any workflow can be saved to a file and then applied to other datasets either using SplitsTree App or using an accompanying command-line workflow runner program.
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<img width="800" alt="image" src="https://github.com/husonlab/splitstree6/blob/main/artwork/example.png">
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<img width="800" alt="example" src="artwork/example.png">
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## History
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Our previous program, SplitsTree4, was designed for computing phylogenetic trees and networks from distances or aligned sequences. It was written in the early 2000's by Daniel Huson and Dave Bryant and described in [(Huson and Bryant, 2006)](https://academic.oup.com/mbe/article/23/2/254/1118872). While the program is still widely used and cited, it was designed for small datasets and the user interface, implemented using the Java Swing library, now feels minimalistic and dated. Moreover, SplitsTree4 was not designed as an open source program.

‎installer/splitstree6.install4j

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<?xml version="1.0" encoding="UTF-8"?>
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<install4j version="10.0.6" transformSequenceNumber="10">
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<directoryPresets config="../target/SplitsTreeApp-1.0.0-SNAPSHOT.jar" />
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<application name="SplitsTreeCE" applicationId="5610-7746-7010-9445" mediaDir="../../../builds" shortName="SplitsTreeCE" publisher="Daniel Huson and David Bryant" publisherWeb="https://www.splitstree.org" version="0.0.0_beta" allPathsRelative="true" macVolumeId="b8c0a1154e563a9a" javaMinVersion="16">
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<application name="SplitsTreeApp" applicationId="5610-7746-7010-9445" mediaDir="../../../builds" shortName="SplitsTreeApp" publisher="Daniel H. Huson and David Bryant" publisherWeb="https://www.splitstree.org" version="0.0.0_beta" allPathsRelative="true" macVolumeId="b8c0a1154e563a9a" javaMinVersion="16">
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<variables>
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<variable name="renderingVMOption" />
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</variables>
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<entry location="install4j-runtime-10.0.5.jar" />
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</exclude>
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</dirEntry>
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<fileEntry mountPoint="1691242167" file="../target/SplitsTreeCE-1.0.0-SNAPSHOT.jar" />
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<fileEntry mountPoint="1691242167" file="../target/SplitsTreeApp-1.0.0-SNAPSHOT.jar" />
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<fileEntry mountPoint="1691243203" file="../target/dependency/install4j-runtime-10.0.5.jar" />
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<dirEntry mountPoint="1691242153" file="../examples" subDirectory="examples" />
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<fileEntry mountPoint="1691243205" file="../tools/genome-context" fileMode="755" overrideFileMode="true" />
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<fileEntry mountPoint="675425072" file="../src/main/resources/NOTICE.txt" />
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</entries>
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<components>
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<component name="SplitsTreeCE" id="1691242194" changeable="false">
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<description>SplitsTree CE program.</description>
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<component name="SplitsTreeApp" id="1691242194" changeable="false">
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<description>The SplitsTree App.</description>
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<include>
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<entry location="jars" />
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<entry location="jars2" />
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<entry location="tools" />
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<entry location="Licenses" />
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<entry location="LICENSE.txt" />
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<entry location="NOTICE.txt" />
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<entry location="SplitsTreeCE" fileType="launcher" />
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<entry location="SplitsTreeApp" fileType="launcher" />
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</include>
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</component>
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<component name="Examples" id="1691243204">
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</components>
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</files>
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<launchers>
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<launcher name="SplitsTreeCE" id="1691242142" menuName="SplitsTree CE ">
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<executable name="SplitsTreeCE" iconSet="true" redirectStdout="true" executableMode="gui" singleInstance="true" checkConsoleParameter="true" dpiAware="false">
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<versionInfo include="true" fileDescription="SplitsTree CE analysis of phylogenetic trees and networks" legalCopyright="Copyright (C) 2024 ${compiler:sys.publisher}" internalName="SplitsTreeCE" />
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<launcher name="SplitsTreeApp" id="1691242142" menuName="SplitsTree App ">
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<executable name="SplitsTreeApp" iconSet="true" redirectStdout="true" executableMode="gui" singleInstance="true" checkConsoleParameter="true" dpiAware="false">
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<versionInfo include="true" fileDescription="SplitsTree app - analysis of phylogenetic trees and networks" legalCopyright="Copyright (C) 2024 ${compiler:sys.publisher}" internalName="SplitsTreeApp" />
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</executable>
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<java mainClass="splitstreesix/splitstree6.main.SplitsTree6" mainMode="module" vmParameters="-server -Duser.language=en -Duser.region=US ${compiler:renderingVMOption}">
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<modulePath>
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<screen id="1691242246" beanClass="com.install4j.runtime.beans.screens.FormScreen">
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<serializedBean>
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<property name="subTitle" type="string">Check for updates how often?</property>
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<property name="title" type="string">SplitsTree CE Updater</property>
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<property name="title" type="string">SplitsTree App Updater</property>
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</serializedBean>
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<formComponents>
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<formComponent id="1691242248" beanClass="com.install4j.runtime.beans.formcomponents.UpdateScheduleSelectorComponent" />
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</formComponents>
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</screen>
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<screen id="1691242249" beanClass="com.install4j.runtime.beans.screens.FormScreen">
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<serializedBean>
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<property name="subTitle" type="string">Set maximum allowed memory usage for SplitsTree CE </property>
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<property name="title" type="string">Set SplitsTree CE memory</property>
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<property name="subTitle" type="string">Set maximum allowed memory usage for SplitsTree App </property>
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<property name="title" type="string">Set SplitsTree App memory</property>
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</serializedBean>
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<condition> !context.getMediaName().toLowerCase().contains("windows") || context.getMediaName().toLowerCase().contains("x64") || context.getMediaName().toLowerCase().contains("64bits") </condition>
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<actions>
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<formComponents>
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<formComponent id="1691242250" beanClass="com.install4j.runtime.beans.formcomponents.NumberSpinnerComponent">
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<serializedBean>
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<property name="helpText" type="string">Set maximum amount of memory that SplitsTree CE may use.</property>
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<property name="helpText" type="string">Set maximum amount of memory that SplitsTree App may use.</property>
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<property name="initialValue" type="int" value="2" />
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<property name="labelText" type="string">Set max memory usage (in gigabytes)</property>
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<property name="maxValue" type="int" value="512" />
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<variable name="renderingVMOption" value="-Dprism.forceGPU=true" />
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</variables>
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</unixInstaller>
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<macosFolder name="Mac OS X Folder" id="1691242165" installDir="SplitsTreeCE" overridePrincipalLanguage="true" architecture="universal" compressDmg="true" signLaunchers="true" />
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<windows name="Windows64bit" id="1691242288" installDir="SplitsTreeCE" overridePrincipalLanguage="true" architecture="64">
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<macosFolder name="Mac OS X Folder" id="1691242165" installDir="SplitsTreeApp" overridePrincipalLanguage="true" architecture="universal" compressDmg="true" signLaunchers="true" />
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<windows name="Windows64bit" id="1691242288" installDir="SplitsTreeApp" overridePrincipalLanguage="true" architecture="64">
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<overriddenPrincipalLanguage id="409" />
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<exclude>
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<entry location="tools" />

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