Skip to content

Commit

Permalink
Add wnv all-lineages dataset
Browse files Browse the repository at this point in the history
  • Loading branch information
corneliusroemer committed Apr 4, 2024
1 parent f6f8687 commit de08f78
Show file tree
Hide file tree
Showing 8 changed files with 477 additions and 0 deletions.
3 changes: 3 additions & 0 deletions data/nextstrain/wnv/all-lineages/CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
## Unreleased

Initial release of this dataset.
24 changes: 24 additions & 0 deletions data/nextstrain/wnv/all-lineages/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
# Nextclade dataset for West Nile virus

| Key | Value |
| ---------------------- | ------------------------------------------------------------------------------------------------------------------------ |
| authors | [Cornelius Roemer](https://neherlab.org), [Richard Neher](https://neherlab.org), [Nextstrain](https://nextstrain.org) |
| data source | Genbank |
| workflow | [github.com/neherlab/nextclade_data_workflows/west-nile](https://github.com/neherlab/nextclade_data_workflows/west-nile) |
| nextclade dataset path | nextstrain/west-nile |
| annotation | [NC_009942.1](https://www.ncbi.nlm.nih.gov/nuccore/NC_009942) |
| clade definitions | from genomedetective.com: <https://www.genomedetective.com/app/typingtool/wnv/introduction> |

## Scope of this dataset

This dataset is intended to be used to classify West Nile virus sequences into major lineages.

## Reference sequence and reference tree

The reference used in this dataset is the lineage 1A NCBI refseq `NC_009942.1` (Isolate `NY99`).

The reference tree consists of around 100 sequences with representatives from all 8 lineages.

## Further reading

Read more about Nextclade datasets in Nextclade documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
182 changes: 182 additions & 0 deletions data/nextstrain/wnv/all-lineages/examples.fasta

Large diffs are not rendered by default.

18 changes: 18 additions & 0 deletions data/nextstrain/wnv/all-lineages/genome_annotation.gff3
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
##sequence-region NC_009942.1 1 11029
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=11082
NC_009942.1 RefSeq region 1 11029 . + . ID=NC_009942.1:1..11029;Dbxref=taxon:11082;country=USA;gb-acronym=WNV;gbkey=Src;genome=genomic;isolate=385-99;mol_type=genomic RNA;note=lineage 1%3B Vero cell passage 2 after isolation;strain=NY99
NC_009942.1 RefSeq gene 97 10395 . + . gene=POLY;ID=gene-WNVNY99_gp1;gbkey=Prot;product=anchored capsid protein ancC;protein_id=YP_005097850.1
NC_009942.1 RefSeq CDS 97 465 . + . gene=capsid;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=anchored capsid protein ancC;protein_id=YP_005097850.1
NC_009942.1 RefSeq CDS 466 966 . + . gene=prM;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=protein pr;protein_id=YP_009164953.1
NC_009942.1 RefSeq CDS 967 2469 . + . gene=env;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=envelope protein E;protein_id=YP_001527880.1
NC_009942.1 RefSeq CDS 2470 3525 . + . gene=NS1;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS1;protein_id=YP_001527881.1
NC_009942.1 RefSeq CDS 3526 4218 . + . gene=NS2A;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS2A;protein_id=YP_001527882.1
NC_009942.1 RefSeq CDS 4219 4611 . + . gene=NS2B;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS2B;protein_id=YP_001527883.1
NC_009942.1 RefSeq CDS 4612 6468 . + . gene=NS3;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS3;protein_id=YP_001527884.1
NC_009942.1 RefSeq CDS 6469 6846 . + . gene=NS4A;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS4A;protein_id=YP_001527885.1
NC_009942.1 RefSeq CDS 6847 6915 . + . gene=2K;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=protein 2K;protein_id=YP_001527885.1
NC_009942.1 RefSeq CDS 6916 7680 . + . gene=NS4B;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=nonstructural protein NS4B;protein_id=YP_001527886.1
NC_009942.1 RefSeq CDS 7681 10395 . + . gene=NS5;Parent=gene-WNVNY99_gp1;gbkey=Prot;product=RNA-dependent RNA polymerase NS5;protein_id=YP_001527887.1
72 changes: 72 additions & 0 deletions data/nextstrain/wnv/all-lineages/pathogen.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,72 @@
{
"alignmentParams": {
"excessBandwidth": 40,
"terminalBandwidth": 200,
"allowedMismatches": 5,
"windowSize": 30,
"minSeedCover": 0.01,
"gapAlignmentSide": "left"
},
"attributes": {
"name": "West Nile Virus",
"reference accession": "NC_009942.1",
"reference name": "Strain NY99 (lineage 1A)"
},
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
},
"deprecated": false,
"enabled": true,
"experimental": false,
"files": {
"changelog": "CHANGELOG.md",
"examples": "examples.fasta",
"genomeAnnotation": "genome_annotation.gff3",
"pathogenJson": "pathogen.json",
"readme": "README.md",
"reference": "reference.fasta",
"treeJson": "tree.json"
},
"official": true,
"qc": {
"frameShifts": {
"enabled": true,
"scoreWeight": 20
},
"missingData": {
"enabled": true,
"missingDataThreshold": 20000,
"scoreBias": 1000
},
"mixedSites": {
"enabled": true,
"mixedSitesThreshold": 40
},
"privateMutations": {
"cutoff": 200,
"enabled": true,
"typical": 50,
"weightLabeledSubstitutions": 1,
"weightReversionSubstitutions": 2,
"weightUnlabeledSubstitutions": 1
},
"snpClusters": {
"clusterCutOff": 5,
"enabled": false,
"scoreWeight": 20,
"windowSize": 100
},
"stopCodons": {
"enabled": true,
"scoreWeight": 40
}
},
"schemaVersion": "3.0.0",
"shortcuts": [
"wnv", "west-nile", "west-nile-virus"
],
"version": {
"tag": "unreleased"
}
}
159 changes: 159 additions & 0 deletions data/nextstrain/wnv/all-lineages/reference.fasta
Original file line number Diff line number Diff line change
@@ -0,0 +1,159 @@
>NC_009942.1 West Nile virus lineage 1, complete genome
AGTAGTTCGCCTGTGTGAGCTGACAAACTTAGTAGTGTTTGTGAGGATTAACAACAATTAACACAGTGCG
AGCTGTTTCTTAGCACGAAGATCTCGATGTCTAAGAAACCAGGAGGGCCCGGCAAGAGCCGGGCTGTCAA
TATGCTAAAACGCGGAATGCCCCGCGTGTTGTCCTTGATTGGACTGAAGAGGGCTATGTTGAGCCTGATC
GACGGCAAGGGGCCAATACGATTTGTGTTGGCTCTCTTGGCGTTCTTCAGGTTCACAGCAATTGCTCCGA
CCCGAGCAGTGCTGGATCGATGGAGAGGTGTGAACAAACAAACAGCGATGAAACACCTTCTGAGTTTTAA
GAAGGAACTAGGGACCTTGACCAGTGCTATCAATCGGCGGAGCTCAAAACAAAAGAAAAGAGGAGGAAAG
ACCGGAATTGCAGTCATGATTGGCCTGATCGCCAGCGTAGGAGCAGTTACCCTCTCTAACTTCCAAGGGA
AGGTGATGATGACGGTAAATGCTACTGACGTCACAGATGTCATCACGATTCCAACAGCTGCTGGAAAGAA
CCTATGCATTGTCAGAGCAATGGATGTGGGATACATGTGCGATGATACTATCACTTATGAATGCCCAGTA
CTGTCGGCTGGTAATGATCCAGAAGACATCGACTGTTGGTGCACAAAGTCAGCAGTCTACGTCAGGTATG
GAAGATGCACCAAGACACGCCACTCAAGACGCAGTCGGAGGTCACTGACAGTGCAGACACACGGAGAAAG
CACTCTAGCGAACAAGAAGGGGGCTTGGATGGACAGCACCAAGGCCACAAGGTATTTGGTAAAAACAGAA
TCATGGATCTTGAGGAACCCTGGATATGCCCTGGTGGCAGCCGTCATTGGTTGGATGCTTGGGAGCAACA
CCATGCAGAGAGTTGTGTTTGTCGTGCTATTGCTTTTGGTGGCCCCAGCTTACAGCTTCAACTGCCTTGG
AATGAGCAACAGAGACTTCTTGGAAGGAGTGTCTGGAGCAACATGGGTGGATTTGGTTCTCGAAGGCGAC
AGCTGCGTGACTATCATGTCTAAGGACAAGCCTACCATCGATGTGAAGATGATGAATATGGAGGCGGCCA
ACCTGGCAGAGGTCCGCAGTTATTGCTATTTGGCTACCGTCAGCGATCTCTCCACCAAAGCTGCGTGCCC
GACCATGGGAGAAGCTCACAATGACAAACGTGCTGACCCAGCTTTTGTGTGCAGACAAGGAGTGGTGGAC
AGGGGCTGGGGCAACGGCTGCGGACTATTTGGCAAAGGAAGCATTGACACATGCGCCAAATTTGCCTGCT
CTACCAAGGCAATAGGAAGAACCATCTTGAAAGAGAATATCAAGTACGAAGTGGCCATTTTTGTCCATGG
ACCAACTACTGTGGAGTCGCACGGAAACTACTCCACACAGGTTGGAGCCACTCAGGCAGGGAGACTCAGC
ATCACTCCTGCGGCGCCTTCATACACACTAAAGCTTGGAGAATATGGAGAGGTGACAGTGGACTGTGAAC
CACGGTCAGGGATTGACACCAATGCATACTACGTGATGACTGTTGGAACAAAGACGTTCTTGGTCCATCG
TGAGTGGTTCATGGACCTCAACCTCCCTTGGAGCAGTGCTGGAAGTACTGTGTGGAGGAACAGAGAGACG
TTAATGGAGTTTGAGGAACCACACGCCACGAAGCAGTCTGTGATAGCATTGGGCTCACAAGAGGGAGCTC
TGCATCAAGCTTTGGCTGGAGCCATTCCTGTGGAATTTTCAAGCAACACTGTCAAGTTGACGTCGGGTCA
TTTGAAGTGTAGAGTGAAGATGGAAAAATTGCAGTTGAAGGGAACAACCTATGGCGTCTGTTCAAAGGCT
TTCAAGTTTCTTGGGACTCCCGCAGACACAGGTCACGGCACTGTGGTGTTGGAATTGCAGTACACTGGCA
CGGATGGACCTTGCAAAGTTCCTATCTCGTCAGTGGCTTCATTGAACGACCTAACGCCAGTGGGCAGATT
GGTCACTGTCAACCCTTTTGTTTCAGTGGCCACGGCCAACGCTAAGGTCCTGATTGAATTGGAACCACCC
TTTGGAGACTCATACATAGTGGTGGGCAGAGGAGAACAACAGATCAATCACCATTGGCACAAGTCTGGAA
GCAGCATTGGCAAAGCCTTTACAACCACCCTCAAAGGAGCGCAGAGACTAGCCGCTCTAGGAGACACAGC
TTGGGACTTTGGATCAGTTGGAGGGGTGTTCACCTCAGTTGGGAAGGCTGTCCATCAAGTGTTCGGAGGA
GCATTCCGCTCACTGTTCGGAGGCATGTCCTGGATAACGCAAGGATTGCTGGGGGCTCTCCTGTTGTGGA
TGGGCATCAATGCTCGTGATAGGTCCATAGCTCTCACGTTTCTCGCAGTTGGAGGAGTTCTGCTCTTCCT
CTCCGTGAACGTGCACGCTGACACTGGGTGTGCCATAGACATCAGCCGGCAAGAGCTGAGATGTGGAAGT
GGAGTGTTCATACACAATGATGTGGAGGCTTGGATGGACCGGTACAAGTATTACCCTGAAACGCCACAAG
GCCTAGCCAAGATCATTCAGAAAGCTCATAAGGAAGGAGTGTGCGGTCTACGATCAGTTTCCAGACTGGA
GCATCAAATGTGGGAAGCAGTGAAGGACGAGCTGAACACTCTTTTGAAGGAGAATGGTGTGGACCTTAGT
GTCGTGGTTGAGAAACAGGAGGGAATGTACAAGTCAGCACCTAAACGCCTCACCGCCACCACGGAAAAAT
TGGAAATTGGCTGGAAGGCCTGGGGAAAGAGTATTTTATTTGCACCAGAACTCGCCAACAACACCTTTGT
GGTTGATGGTCCGGAGACCAAGGAATGTCCGACTCAGAATCGCGCTTGGAATAGCTTAGAAGTGGAGGAT
TTTGGATTTGGTCTCACCAGCACTCGGATGTTCCTGAAGGTCAGAGAGAGCAACACAACTGAATGTGACT
CGAAGATCATTGGAACGGCTGTCAAGAACAACTTGGCGATCCACAGTGACCTGTCCTATTGGATTGAAAG
CAGGCTCAATGATACGTGGAAGCTTGAAAGGGCAGTTCTGGGTGAAGTCAAATCATGTACGTGGCCTGAG
ACGCATACCTTGTGGGGCGATGGAATCCTTGAGAGTGACTTGATAATACCAGTCACACTGGCGGGACCAC
GAAGCAATCACAATCGGAGACCTGGGTACAAGACACAAAACCAGGGCCCATGGGACGAAGGCCGGGTAGA
GATTGACTTCGATTACTGCCCAGGAACTACGGTCACCCTGAGTGAGAGCTGCGGACACCGTGGACCTGCC
ACTCGCACCACCACAGAGAGCGGAAAGTTGATAACAGATTGGTGCTGCAGGAGCTGCACCTTACCACCAC
TGCGCTACCAAACTGACAGCGGCTGTTGGTATGGTATGGAGATCAGACCACAGAGACATGATGAAAAGAC
CCTCGTGCAGTCACAAGTGAATGCTTATAATGCTGATATGATTGACCCTTTTCAGTTGGGCCTTCTGGTC
GTGTTCTTGGCCACCCAGGAGGTCCTTCGCAAGAGGTGGACAGCCAAGATCAGCATGCCAGCTATACTGA
TTGCTCTGCTAGTCCTGGTGTTTGGGGGCATTACTTACACTGATGTGTTACGCTATGTCATCTTGGTGGG
GGCAGCTTTCGCAGAATCTAATTCGGGAGGAGACGTGGTACACTTGGCGCTCATGGCGACCTTCAAGATA
CAACCAGTGTTTATGGTGGCATCGTTTCTCAAAGCGAGATGGACCAACCAGGAGAACATTTTGTTGATGT
TGGCGGCTGTTTTCTTTCAAATGGCTTATCACGATGCCCGCCAAATTCTGCTCTGGGAGATCCCTGATGT
GTTGAATTCACTGGCGGTAGCTTGGATGATACTGAGAGCCATAACATTCACAACGACATCAAACGTGGTT
GTTCCGCTGCTAGCCCTGCTAACACCCGGGCTGAGATGCTTGAATCTGGATGTGTACAGGATACTGCTGT
TGATGGTCGGAATAGGCAGCTTGATCAGGGAGAAGAGGAGTGCAGCCGCAAAAAAGAAAGGAGCAAGTCT
GCTATGCTTGGCTCTAGCCTCAACAGGACTTTTCAACCCCATGATCCTTGCTGCTGGACTGATTGCATGT
GATCCCAACCGTAAACGCGGATGGCCCGCAACTGAAGTGATGACAGCTGTCGGCCTAATGTTTGCCATCG
TCGGAGGGCTGGCAGAGCTTGACATTGACTCCATGGCCATTCCAATGACTATCGCGGGGCTCATGTTTGC
TGCTTTCGTGATTTCTGGGAAATCAACAGATATGTGGATTGAGAGAACGGCGGACATTTCCTGGGAAAGT
GATGCAGAAATTACAGGCTCGAGCGAAAGAGTTGATGTGCGGCTTGATGATGATGGAAACTTCCAGCTCA
TGAATGATCCAGGAGCACCTTGGAAGATATGGATGCTCAGAATGGTCTGTCTCGCGATTAGTGCGTACAC
CCCCTGGGCAATCTTGCCCTCAGTAGTTGGATTTTGGATAACTCTCCAATACACAAAGAGAGGAGGCGTG
TTGTGGGACACTCCCTCACCAAAGGAGTACAAAAAGGGGGACACGACCACCGGCGTCTACAGGATCATGA
CTCGTGGGCTGCTCGGCAGTTATCAAGCAGGAGCGGGCGTGATGGTTGAAGGTGTTTTCCACACCCTTTG
GCATACAACAAAAGGAGCCGCTTTGATGAGCGGAGAGGGCCGCCTGGACCCATACTGGGGCAGTGTCAAG
GAGGATCGACTTTGTTACGGAGGACCCTGGAAATTGCAGCACAAGTGGAACGGGCAGGATGAGGTGCAGA
TGATTGTGGTGGAACCTGGCAAGAACGTTAAGAACGTCCAGACGAAACCAGGGGTGTTCAAAACACCTGA
AGGAGAAATCGGGGCCGTGACTTTGGACTTCCCCACTGGAACATCAGGCTCACCAATAGTGGACAAAAAC
GGTGATGTGATTGGGCTTTATGGCAATGGAGTCATAATGCCCAACGGCTCATACATAAGCGCGATAGTGC
AGGGTGAAAGGATGGATGAGCCAATCCCAGCCGGATTCGAACCTGAGATGCTGAGGAAAAAACAGATCAC
TGTACTGGATCTCCATCCCGGCGCCGGTAAAACAAGGAGGATTCTGCCACAGATCATCAAAGAGGCCATA
AACAGAAGACTGAGAACAGCCGTGCTAGCGCCAACCAGGGTTGTGGCTGCTGAGATGGCTGAAGCACTGA
GAGGACTGCCCATCCGGTACCAGACATCCGCAGTGCCCAGAGAACATAATGGAAATGAGATTGTTGATGT
CATGTGTCATGCTACCCTCACCCACAGGCTGATGTCTCCTCACAGGGTGCCGAACTACAACCTGTTCGTG
ATGGATGAGGCTCATTTCACCGACCCAGCTAGCATTGCAGCAAGAGGTTACATTTCCACAAAGGTCGAGC
TAGGGGAGGCGGCGGCAATATTCATGACAGCCACCCCACCAGGCACTTCAGATCCATTCCCAGAGTCCAA
TTCACCAATTTCCGACTTACAGACTGAGATCCCGGATCGAGCTTGGAACTCTGGATACGAATGGATCACA
GAATACACCGGGAAGACGGTTTGGTTTGTGCCTAGTGTCAAGATGGGGAATGAGATTGCCCTTTGCCTAC
AACGTGCTGGAAAGAAAGTAGTCCAATTGAACAGAAAGTCGTACGAGACGGAGTACCCAAAATGTAAGAA
CGATGATTGGGACTTTGTTATCACAACAGACATATCTGAAATGGGGGCTAACTTCAAGGCGAGCAGGGTG
ATTGACAGCCGGAAGAGTGTGAAACCAACCATCATAACAGAAGGAGAAGGGAGAGTGATCCTGGGAGAAC
CATCTGCAGTGACAGCAGCTAGTGCCGCCCAGAGACGTGGACGTATCGGTAGAAATCCGTCGCAAGTTGG
TGATGAGTACTGTTATGGGGGGCACACGAATGAAGACGACTCGAACTTCGCCCATTGGACTGAGGCACGA
ATCATGCTGGACAACATCAACATGCCAAACGGACTGATCGCTCAATTCTACCAACCAGAGCGTGAGAAGG
TATATACCATGGATGGGGAATACCGGCTCAGAGGAGAAGAGAGAAAAAACTTTCTGGAACTGTTGAGGAC
TGCAGATCTGCCAGTTTGGCTGGCTTACAAGGTTGCAGCGGCTGGAGTGTCATACCACGACCGGAGGTGG
TGCTTTGATGGTCCTAGGACAAACACAATTTTAGAAGACAACAACGAAGTGGAAGTCATCACGAAGCTTG
GTGAAAGGAAGATTCTGAGGCCGCGCTGGATTGATGCCAGGGTGTACTCGGATCACCAGGCACTAAAGGC
GTTCAAGGACTTCGCCTCGGGAAAACGTTCTCAGATAGGGCTCATTGAGGTTCTGGGAAAGATGCCTGAG
CACTTCATGGGGAAGACATGGGAAGCACTTGACACCATGTACGTTGTGGCCACTGCAGAGAAAGGAGGAA
GAGCTCACAGAATGGCCCTGGAGGAACTGCCAGATGCTCTTCAGACAATTGCCTTGATTGCCTTATTGAG
TGTGATGACCATGGGAGTATTCTTCCTCCTCATGCAGCGGAAGGGCATTGGAAAGATAGGTTTGGGAGGC
GCTGTCTTGGGAGTCGCGACCTTTTTCTGTTGGATGGCTGAAGTTCCAGGAACGAAGATCGCCGGAATGT
TGCTGCTCTCCCTTCTCTTGATGATTGTGCTAATTCCTGAGCCAGAGAAGCAACGTTCGCAGACAGACAA
CCAGCTAGCCGTGTTCCTGATTTGTGTCATGACCCTTGTGAGCGCAGTGGCAGCCAACGAGATGGGTTGG
CTAGATAAGACCAAGAGTGACATAAGCAGTTTGTTTGGGCAAAGAATTGAGGTCAAGGAGAATTTCAGCA
TGGGAGAGTTTCTTCTGGACTTGAGGCCGGCAACAGCCTGGTCACTGTACGCTGTGACAACAGCGGTCCT
CACTCCACTGCTAAAGCATTTGATCACGTCAGATTACATCAACACCTCATTGACCTCAATAAACGTTCAG
GCAAGTGCACTATTCACACTCGCGCGAGGCTTCCCCTTCGTCGATGTTGGAGTGTCGGCTCTCCTGCTAG
CAGCCGGATGCTGGGGACAAGTCACCCTCACCGTTACGGTAACAGCGGCAACACTCCTTTTTTGCCACTA
TGCCTACATGGTTCCCGGTTGGCAAGCTGAGGCAATGCGCTCAGCCCAGCGGCGGACAGCGGCCGGAATC
ATGAAGAACGCTGTAGTGGATGGCATCGTGGCCACGGACGTCCCAGAATTAGAGCGCACCACACCCATCA
TGCAGAAGAAAGTTGGACAGATCATGCTGATCTTGGTGTCTCTAGCTGCAGTAGTAGTGAACCCGTCTGT
GAAGACAGTACGAGAAGCCGGAATTTTGATCACGGCCGCAGCGGTGACGCTTTGGGAGAATGGAGCAAGC
TCTGTTTGGAACGCAACAACTGCCATCGGACTCTGCCACATCATGCGTGGGGGTTGGTTGTCATGTCTAT
CCATAACATGGACACTCATAAAGAACATGGAAAAACCAGGACTAAAAAGAGGTGGGGCAAAAGGACGCAC
CTTGGGAGAGGTTTGGAAAGAAAGACTCAACCAGATGACAAAAGAAGAGTTCACTAGGTACCGCAAAGAG
GCCATCATCGAAGTCGATCGCTCAGCGGCAAAACACGCCAGGAAAGAAGGCAATGTCACTGGAGGGCATC
CAGTCTCTAGGGGCACAGCAAAACTGAGATGGCTGGTCGAACGGAGGTTTCTCGAACCGGTCGGAAAAGT
GATTGACCTTGGATGTGGAAGAGGCGGTTGGTGTTACTATATGGCAACCCAAAAAAGAGTCCAAGAAGTC
AGAGGGTACACAAAGGGCGGTCCCGGACATGAAGAGCCCCAACTAGTGCAAAGTTATGGATGGAACATTG
TCACCATGAAGAGTGGAGTGGATGTGTTCTACAGACCTTCTGAGTGTTGTGACACCCTCCTTTGTGACAT
CGGAGAGTCCTCGTCAAGTGCTGAGGTTGAAGAGCATAGGACGATTCGGGTCCTTGAAATGGTTGAGGAC
TGGCTGCACCGAGGGCCAAGGGAATTTTGCGTGAAGGTGCTCTGTCCCTACATGCCGAAAGTCATAGAGA
AGATGGAGCTGCTCCAACGCCGGTATGGGGGGGGACTGGTCAGAAACCCACTCTCACGGAATTCCACGCA
CGAGATGTATTGGGTGAGTCGAGCTTCAGGCAATGTGGTACATTCAGTGAATATGACCAGCCAGGTGCTC
CTAGGAAGAATGGAAAAAAGGACCTGGAAGGGACCCCAATACGAGGAAGATGTAAACTTGGGAAGTGGAA
CCAGGGCGGTGGGAAAACCCCTGCTCAACTCAGACACCAGTAAAATCAAGAACAGGATTGAACGACTCAG
GCGTGAGTACAGTTCGACGTGGCACCACGATGAGAACCACCCATATAGAACCTGGAACTATCACGGCAGT
TATGATGTGAAGCCCACAGGCTCCGCCAGTTCGCTGGTCAATGGAGTGGTCAGGCTCCTCTCAAAACCAT
GGGACACCATCACGAATGTTACCACCATGGCCATGACTGACACTACTCCCTTCGGGCAGCAGCGAGTGTT
CAAAGAGAAGGTGGACACGAAAGCTCCTGAACCGCCAGAAGGAGTGAAGTACGTGCTCAACGAGACCACC
AACTGGTTGTGGGCGTTTTTGGCCAGAGAAAAACGTCCCAGAATGTGCTCTCGAGAGGAATTCATAAGAA
AGGTCAACAGCAATGCAGCTTTGGGTGCCATGTTTGAAGAGCAGAATCAATGGAGGAGCGCCAGAGAAGC
AGTTGAAGATCCAAAATTTTGGGAGATGGTGGATGAGGAGCGCGAGGCACATCTGCGGGGGGAATGTCAC
ACTTGCATTTACAACATGATGGGAAAGAGAGAGAAAAAACCCGGAGAGTTCGGAAAGGCCAAGGGAAGCA
GAGCCATTTGGTTCATGTGGCTCGGAGCTCGCTTTCTGGAGTTCGAGGCTCTGGGTTTTCTCAATGAAGA
CCACTGGCTTGGAAGAAAGAACTCAGGAGGAGGTGTCGAGGGCTTGGGCCTCCAAAAACTGGGTTACATC
CTGCGTGAAGTTGGCACCCGGCCTGGGGGCAAGATCTATGCTGATGACACAGCTGGCTGGGACACCCGCA
TCACGAGAGCTGACTTGGAAAATGAAGCTAAGGTGCTTGAGCTGCTTGATGGGGAACATCGGCGTCTTGC
CAGGGCCATCATTGAGCTCACCTATCGTCACAAAGTTGTGAAAGTGATGCGCCCGGCTGCTGATGGAAGA
ACCGTCATGGATGTTATCTCCAGAGAAGATCAGAGGGGGAGTGGACAAGTTGTCACCTACGCCCTAAACA
CTTTCACCAACCTGGCCGTCCAGCTGGTGAGGATGATGGAAGGGGAAGGAGTGATTGGCCCAGATGATGT
GGAGAAACTCACAAAAGGGAAAGGACCCAAAGTCAGGACCTGGCTGTTTGAGAATGGGGAAGAAAGACTC
AGCCGCATGGCTGTCAGTGGAGATGACTGTGTGGTAAAGCCCCTGGACGATCGCTTTGCCACCTCGCTCC
ACTTCCTCAATGCTATGTCAAAGGTTCGCAAAGACATCCAAGAGTGGAAACCGTCAACTGGATGGTATGA
TTGGCAGCAGGTTCCATTTTGCTCAAACCATTTCACTGAATTGATCATGAAAGATGGAAGAACACTGGTG
GTTCCATGCCGAGGACAGGATGAATTGGTAGGCAGAGCTCGCATATCTCCAGGGGCCGGATGGAACGTCC
GCGACACTGCTTGTCTGGCTAAGTCTTATGCCCAGATGTGGCTGCTTCTGTACTTCCACAGAAGAGACCT
GCGGCTCATGGCCAACGCCATTTGCTCCGCTGTCCCTGTGAATTGGGTCCCTACCGGAAGAACCACGTGG
TCCATCCATGCAGGAGGAGAGTGGATGACAACAGAGGACATGTTGGAGGTCTGGAACCGTGTTTGGATAG
AGGAGAATGAATGGATGGAAGACAAAACCCCAGTGGAGAAATGGAGTGACGTCCCATATTCAGGAAAACG
AGAGGACATCTGGTGTGGCAGCCTGATTGGCACAAGAGCCCGAGCCACGTGGGCAGAAAACATCCAGGTG
GCTATCAACCAAGTCAGAGCAATCATCGGAGATGAGAAGTATGTGGACTACATGAGTTCACTAAAGAGAT
ATGAAGACACAACTTTGGTTGAGGACACAGTACTGTAGATATTTAATCAATTGTAAATAGACAATATAAG
TATGCATAAAAGTGTAGTTTTATAGTAGTATTTAGTGGTGTTAGTGTAAATAGTTAAGAAAATTTTGAGG
AGAAAGTCAGGCCGGGAAGTTCCCGCCACCGGAAGTTGAGTAGACGGTGCTGCCTGCGACTCAACCCCAG
GAGGACTGGGTGAACAAAGCCGCGAAGTGATCCATGTAAGCCCTCAGAACCGTCTCGGAAGGAGGACCCC
ACATGTTGTAACTTCAAAGCCCAATGTCAGACCACGCTACGGCGTGCTACTCTGCGGAGAGTGCAGTCTG
CGATAGTGCCCCAGGAGGACTGGGTTAACAAAGGCAAACCAACGCCCCACGCGGCCCTAGCCCCGGTAAT
GGTGTTAACCAGGGCGAAAGGACTAGAGGTTAGAGGAGACCCCGCGGTTTAAAGTGCACGGCCCAGCCTG
GCTGAAGCTGTAGGTCAGGGGAAGGACTAGAGGTTAGTGGAGACCCCGTGCCACAAAACACCACAACAAA
ACAGCATATTGACACCTGGGATAGACTAGGAGATCTTCTGCTCTGCACAACCAGCCACACGGCACAGTGC
GCCGACAATGGTGGCTGGTGGTGCGAGAACACAGGATCT
18 changes: 18 additions & 0 deletions data/nextstrain/wnv/all-lineages/sequences.fasta

Large diffs are not rendered by default.

1 change: 1 addition & 0 deletions data/nextstrain/wnv/all-lineages/tree.json

Large diffs are not rendered by default.

0 comments on commit de08f78

Please sign in to comment.