diff --git a/README.md b/README.md
index e0d4744c..887291f4 100644
--- a/README.md
+++ b/README.md
@@ -26,19 +26,19 @@ nextstrain build . data/sequences.fasta data/metadata.tsv
 Run pipeline to produce the "overview" tree for `/mpox/all-clades` with:
 
 ```bash
-nextstrain build . --configfile config/config_mpxv.yaml
+nextstrain build . --configfile config/mpxv/config.yaml
 ```
 
 Run pipeline to produce the "clade IIb" tree for `/mpox/clade-IIb` with:
 
 ```bash
-nextstrain build . --configfile config/config_hmpxv1.yaml
+nextstrain build . --configfile config/hmpxv1/config.yaml
 ```
 
 Run pipeline to produce the "lineage B.1" tree for `/mpox/lineage-B.1` with:
 
 ```bash
-nextstrain build . --configfile config/config_hmpxv1_big.yaml
+nextstrain build . --configfile config/hmpxv1_big/config.yaml
 ```
 
 ### Deploying
@@ -73,7 +73,7 @@ nextstrain view .
 
 ## Configuration
 
-Configuration takes place in `config/config_*.yaml` files for each build..
+Configuration takes place in `config/*/config.yaml` files for each build.
 The analysis pipeline is contained in `workflow/snakemake_rule/core.smk`.
 This can be read top-to-bottom, each rule specifies its file inputs and output and pulls its parameters from `config`.
 There is little redirection and each rule should be able to be reasoned with on its own.
@@ -110,18 +110,18 @@ snakemake --configfile config/config_hmpxv1_big.yaml
 
 ### Update colors to include new countries
 
-Update `colors_hmpxv1.tsv` to group countries by region based on countries present in its `metadata.tsv`:
+Update `hmpxv1/colors.tsv` to group countries by region based on countries present in its `metadata.tsv`:
 
 ```bash
-python3 scripts/update_colours.py --colors config/colors_hmpxv1.tsv \
-    --metadata results/hmpxv1/metadata.tsv --output config/colors_hmpxv1.tsv
+python3 scripts/update_colours.py --colors config/hmpxv1/colors.tsv \
+    --metadata results/hmpxv1/metadata.tsv --output config/hmpxv1/colors.tsv
 ```
 
-and similarly update `colors_mpxv.tsv`:
+and similarly update `mpxv/colors.tsv`:
 
 ```bash
-python3 scripts/update_colours.py --colors config/colors_mpxv.tsv \
-    --metadata results/mpxv/metadata.tsv --output config/colors_mpxv.tsv
+python3 scripts/update_colours.py --colors config/mpxv/colors.tsv \
+    --metadata results/mpxv/metadata.tsv --output config/mpxv/colors.tsv
 ```
 
 ### Update example data
diff --git a/config/exclude_accessions_mpxv.txt b/config/exclude_accessions.txt
similarity index 100%
rename from config/exclude_accessions_mpxv.txt
rename to config/exclude_accessions.txt
diff --git a/config/auspice_config_hmpxv1.json b/config/hmpxv1/auspice_config.json
similarity index 100%
rename from config/auspice_config_hmpxv1.json
rename to config/hmpxv1/auspice_config.json
diff --git a/config/colors_hmpxv1.tsv b/config/hmpxv1/colors.tsv
similarity index 100%
rename from config/colors_hmpxv1.tsv
rename to config/hmpxv1/colors.tsv
diff --git a/config/config_hmpxv1.yaml b/config/hmpxv1/config.yaml
similarity index 90%
rename from config/config_hmpxv1.yaml
rename to config/hmpxv1/config.yaml
index 0edb53c2..11bcaa11 100644
--- a/config/config_hmpxv1.yaml
+++ b/config/hmpxv1/config.yaml
@@ -1,10 +1,11 @@
 reference: "config/reference.fasta"
 genemap: "config/genemap.gff"
 genbank_reference: "config/reference.gb"
-colors: "config/colors_hmpxv1.tsv"
+colors: "config/hmpxv1/colors.tsv"
+include: "config/hmpxv1/include.txt"
 clades: "config/clades.tsv"
 lat_longs: "config/lat_longs.tsv"
-auspice_config: "config/auspice_config_hmpxv1.json"
+auspice_config: "config/hmpxv1/auspice_config.json"
 description: "config/description.md"
 tree_mask: "config/tree_mask.tsv"
 
@@ -17,7 +18,7 @@ build_name: "hmpxv1"
 auspice_name: "mpox_clade-IIb"
 
 filter:
-  exclude: "config/exclude_accessions_mpxv.txt"
+  exclude: "config/exclude_accessions.txt"
   min_date: 2017
   min_length: 100000
 
diff --git a/config/include_hmpxv1.txt b/config/hmpxv1/include.txt
similarity index 100%
rename from config/include_hmpxv1.txt
rename to config/hmpxv1/include.txt
diff --git a/config/auspice_config_hmpxv1_big.json b/config/hmpxv1_big/auspice_config.json
similarity index 100%
rename from config/auspice_config_hmpxv1_big.json
rename to config/hmpxv1_big/auspice_config.json
diff --git a/config/config_hmpxv1_big.yaml b/config/hmpxv1_big/config.yaml
similarity index 86%
rename from config/config_hmpxv1_big.yaml
rename to config/hmpxv1_big/config.yaml
index 2b32589c..79d4878f 100644
--- a/config/config_hmpxv1_big.yaml
+++ b/config/hmpxv1_big/config.yaml
@@ -1,10 +1,11 @@
 reference: "config/reference.fasta"
 genemap: "config/genemap.gff"
 genbank_reference: "config/reference.gb"
-colors: "config/colors_hmpxv1.tsv"
+colors: "config/hmpxv1/colors.tsv"
+include: "config/hmpxv1_big/include.txt"
 clades: "config/clades.tsv"
 lat_longs: "config/lat_longs.tsv"
-auspice_config: "config/auspice_config_hmpxv1_big.json"
+auspice_config: "config/hmpxv1_big/auspice_config.json"
 description: "config/description.md"
 tree_mask: "config/tree_mask.tsv"
 
@@ -17,7 +18,7 @@ build_name: "hmpxv1_big"
 auspice_name: "mpox_lineage-B.1"
 
 filter:
-  exclude: "config/exclude_accessions_mpxv.txt"
+  exclude: "config/exclude_accessions.txt"
   min_date: 2022
   min_length: 180000
 
diff --git a/config/include_hmpxv1_big.txt b/config/hmpxv1_big/include.txt
similarity index 100%
rename from config/include_hmpxv1_big.txt
rename to config/hmpxv1_big/include.txt
diff --git a/config/auspice_config_mpxv.json b/config/mpxv/auspice_config.json
similarity index 100%
rename from config/auspice_config_mpxv.json
rename to config/mpxv/auspice_config.json
diff --git a/config/colors_mpxv.tsv b/config/mpxv/colors.tsv
similarity index 100%
rename from config/colors_mpxv.tsv
rename to config/mpxv/colors.tsv
diff --git a/config/config_mpxv.yaml b/config/mpxv/config.yaml
similarity index 90%
rename from config/config_mpxv.yaml
rename to config/mpxv/config.yaml
index ba93fccf..134cea6c 100644
--- a/config/config_mpxv.yaml
+++ b/config/mpxv/config.yaml
@@ -1,9 +1,10 @@
+auspice_config: "config/mpxv/auspice_config.json"
+include: "config/mpxv/include.txt"
+colors: "config/mpxv/colors.tsv"
 reference: "config/reference.fasta"
 genemap: "config/genemap.gff"
 genbank_reference: "config/reference.gb"
-colors: "config/colors_mpxv.tsv"
 lat_longs: "config/lat_longs.tsv"
-auspice_config: "config/auspice_config_mpxv.json"
 description: "config/description.md"
 clades: "config/clades.tsv"
 tree_mask: "config/tree_mask.tsv"
@@ -17,7 +18,7 @@ build_name: "mpxv"
 auspice_name: "mpox_all-clades"
 
 filter:
-  exclude: "config/exclude_accessions_mpxv.txt"
+  exclude: "config/exclude_accessions.txt"
   min_date: 1950
   min_length: 100000
 
diff --git a/config/include_mpxv.txt b/config/mpxv/include.txt
similarity index 100%
rename from config/include_mpxv.txt
rename to config/mpxv/include.txt
diff --git a/profiles/default/config.yaml b/profiles/default/config.yaml
index 4f554b22..43180c5d 100644
--- a/profiles/default/config.yaml
+++ b/profiles/default/config.yaml
@@ -2,4 +2,4 @@ cores: all
 printshellcmds: true
 reason: true
 rerun-incomplete: true
-configfile: config/config_mpxv.yaml
+configfile: config/mpxv/config.yaml
diff --git a/workflow/snakemake_rules/core.smk b/workflow/snakemake_rules/core.smk
index ea9bac8f..0ef1cce3 100644
--- a/workflow/snakemake_rules/core.smk
+++ b/workflow/snakemake_rules/core.smk
@@ -83,7 +83,7 @@ rule combine_samples:
         ],
         sequences=rules.filter.output.sequences,
         metadata=rules.filter.output.metadata,
-        include="config/include_{build_name}.txt",
+        include=config["include"],
     output:
         sequences=build_dir + "/{build_name}/filtered.fasta",
         metadata=build_dir + "/{build_name}/metadata.tsv",