Add example sequences

nextstrain · Aug 13, 2024 · e009a93 · e009a93
1 parent bf9fd0e
commit e009a93
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Showing 29 changed files with 27,111 additions and 4 deletions.
diff --git a/...y/dengue-lineages/all-serotypes/README.md → ...b/dengue-lineages/all-serotypes/README.md b/...y/dengue-lineages/all-serotypes/README.md → ...b/dengue-lineages/all-serotypes/README.md
diff --git a/...lineages/all-serotypes/denv1/CHANGELOG.md → ...lineages/all-serotypes/denv1/CHANGELOG.md b/...lineages/all-serotypes/denv1/CHANGELOG.md → ...lineages/all-serotypes/denv1/CHANGELOG.md
diff --git a/...ue-lineages/all-serotypes/denv1/README.md → ...ue-lineages/all-serotypes/denv1/README.md b/...ue-lineages/all-serotypes/denv1/README.md → ...ue-lineages/all-serotypes/denv1/README.md
diff --git a/...ll-serotypes/denv1/genome_annotation.gff3 → ...ll-serotypes/denv1/genome_annotation.gff3 b/...ll-serotypes/denv1/genome_annotation.gff3 → ...ll-serotypes/denv1/genome_annotation.gff3
diff --git a/...ineages/all-serotypes/denv1/pathogen.json → ...ineages/all-serotypes/denv1/pathogen.json b/...ineages/all-serotypes/denv1/pathogen.json → ...ineages/all-serotypes/denv1/pathogen.json
@@ -25,6 +25,7 @@
   "experimental": true,
   "files": {
     "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
     "genomeAnnotation": "genome_annotation.gff3",
     "pathogenJson": "pathogen.json",
     "readme": "README.md",
@@ -51,7 +52,7 @@
     "privateMutations": {
       "cutoff": 25,
       "enabled": true,
-      "typical": 10,
+      "typical": 15,
       "weightLabeledSubstitutions": 2,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1

diff --git a/...eages/all-serotypes/denv1/reference.fasta → ...eages/all-serotypes/denv1/reference.fasta b/...eages/all-serotypes/denv1/reference.fasta → ...eages/all-serotypes/denv1/reference.fasta
diff --git a/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/sequences.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv1/sequences.fasta
diff --git a/...ue-lineages/all-serotypes/denv1/tree.json → ...ue-lineages/all-serotypes/denv1/tree.json b/...ue-lineages/all-serotypes/denv1/tree.json → ...ue-lineages/all-serotypes/denv1/tree.json
diff --git a/...lineages/all-serotypes/denv2/CHANGELOG.md → ...lineages/all-serotypes/denv2/CHANGELOG.md b/...lineages/all-serotypes/denv2/CHANGELOG.md → ...lineages/all-serotypes/denv2/CHANGELOG.md
diff --git a/...ue-lineages/all-serotypes/denv2/README.md → ...ue-lineages/all-serotypes/denv2/README.md b/...ue-lineages/all-serotypes/denv2/README.md → ...ue-lineages/all-serotypes/denv2/README.md
diff --git a/...ll-serotypes/denv2/genome_annotation.gff3 → ...ll-serotypes/denv2/genome_annotation.gff3 b/...ll-serotypes/denv2/genome_annotation.gff3 → ...ll-serotypes/denv2/genome_annotation.gff3
diff --git a/...ineages/all-serotypes/denv2/pathogen.json → ...ineages/all-serotypes/denv2/pathogen.json b/...ineages/all-serotypes/denv2/pathogen.json → ...ineages/all-serotypes/denv2/pathogen.json
@@ -25,6 +25,7 @@
   "experimental": true,
   "files": {
     "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
     "genomeAnnotation": "genome_annotation.gff3",
     "pathogenJson": "pathogen.json",
     "readme": "README.md",
@@ -51,7 +52,7 @@
     "privateMutations": {
       "cutoff": 25,
       "enabled": true,
-      "typical": 10,
+      "typical": 15,
       "weightLabeledSubstitutions": 2,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1

diff --git a/...eages/all-serotypes/denv2/reference.fasta → ...eages/all-serotypes/denv2/reference.fasta b/...eages/all-serotypes/denv2/reference.fasta → ...eages/all-serotypes/denv2/reference.fasta
diff --git a/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/sequences.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv2/sequences.fasta
diff --git a/...ue-lineages/all-serotypes/denv2/tree.json → ...ue-lineages/all-serotypes/denv2/tree.json b/...ue-lineages/all-serotypes/denv2/tree.json → ...ue-lineages/all-serotypes/denv2/tree.json
diff --git a/...lineages/all-serotypes/denv3/CHANGELOG.md → ...lineages/all-serotypes/denv3/CHANGELOG.md b/...lineages/all-serotypes/denv3/CHANGELOG.md → ...lineages/all-serotypes/denv3/CHANGELOG.md
diff --git a/...ue-lineages/all-serotypes/denv3/README.md → ...ue-lineages/all-serotypes/denv3/README.md b/...ue-lineages/all-serotypes/denv3/README.md → ...ue-lineages/all-serotypes/denv3/README.md
diff --git a/...ll-serotypes/denv3/genome_annotation.gff3 → ...ll-serotypes/denv3/genome_annotation.gff3 b/...ll-serotypes/denv3/genome_annotation.gff3 → ...ll-serotypes/denv3/genome_annotation.gff3
diff --git a/...ineages/all-serotypes/denv3/pathogen.json → ...ineages/all-serotypes/denv3/pathogen.json b/...ineages/all-serotypes/denv3/pathogen.json → ...ineages/all-serotypes/denv3/pathogen.json
@@ -25,6 +25,7 @@
   "experimental": true,
   "files": {
     "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
     "genomeAnnotation": "genome_annotation.gff3",
     "pathogenJson": "pathogen.json",
     "readme": "README.md",
@@ -51,7 +52,7 @@
     "privateMutations": {
       "cutoff": 25,
       "enabled": true,
-      "typical": 10,
+      "typical": 15,
       "weightLabeledSubstitutions": 2,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1

diff --git a/...eages/all-serotypes/denv3/reference.fasta → ...eages/all-serotypes/denv3/reference.fasta b/...eages/all-serotypes/denv3/reference.fasta → ...eages/all-serotypes/denv3/reference.fasta
diff --git a/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/sequences.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv3/sequences.fasta
diff --git a/...ue-lineages/all-serotypes/denv3/tree.json → ...ue-lineages/all-serotypes/denv3/tree.json b/...ue-lineages/all-serotypes/denv3/tree.json → ...ue-lineages/all-serotypes/denv3/tree.json
diff --git a/...lineages/all-serotypes/denv4/CHANGELOG.md → ...lineages/all-serotypes/denv4/CHANGELOG.md b/...lineages/all-serotypes/denv4/CHANGELOG.md → ...lineages/all-serotypes/denv4/CHANGELOG.md
diff --git a/...ue-lineages/all-serotypes/denv4/README.md → ...ue-lineages/all-serotypes/denv4/README.md b/...ue-lineages/all-serotypes/denv4/README.md → ...ue-lineages/all-serotypes/denv4/README.md
diff --git a/...ll-serotypes/denv4/genome_annotation.gff3 → ...ll-serotypes/denv4/genome_annotation.gff3 b/...ll-serotypes/denv4/genome_annotation.gff3 → ...ll-serotypes/denv4/genome_annotation.gff3
diff --git a/...ineages/all-serotypes/denv4/pathogen.json → ...ineages/all-serotypes/denv4/pathogen.json b/...ineages/all-serotypes/denv4/pathogen.json → ...ineages/all-serotypes/denv4/pathogen.json
@@ -25,6 +25,7 @@
   "experimental": true,
   "files": {
     "changelog": "CHANGELOG.md",
+    "examples": "sequences.fasta",
     "genomeAnnotation": "genome_annotation.gff3",
     "pathogenJson": "pathogen.json",
     "readme": "README.md",
@@ -51,7 +52,7 @@
     "privateMutations": {
       "cutoff": 25,
       "enabled": true,
-      "typical": 10,
+      "typical": 15,
       "weightLabeledSubstitutions": 2,
       "weightReversionSubstitutions": 1,
       "weightUnlabeledSubstitutions": 1

diff --git a/...eages/all-serotypes/denv4/reference.fasta → ...eages/all-serotypes/denv4/reference.fasta b/...eages/all-serotypes/denv4/reference.fasta → ...eages/all-serotypes/denv4/reference.fasta
diff --git a/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/sequences.fasta b/data/community/v-gen-lab/dengue-lineages/all-serotypes/denv4/sequences.fasta
diff --git a/...ue-lineages/all-serotypes/denv4/tree.json → ...ue-lineages/all-serotypes/denv4/tree.json b/...ue-lineages/all-serotypes/denv4/tree.json → ...ue-lineages/all-serotypes/denv4/tree.json