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rneher merged 7 commits into from
May 12, 2026
Merged

andv: update datasets #449

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766399b
andv: update datasets
rneher May 12, 2026
aee2b40
chore: rebuild [skip ci]
nextstrain-bot May 12, 2026
bd15790
apply fixes
rneher May 12, 2026
f7f3ce3
remove erroneously committed file
rneher May 12, 2026
c9eda23
chore: rebuild [skip ci]
nextstrain-bot May 12, 2026
a147b8a
andv: update examples
rneher May 12, 2026
d0ba820
chore: rebuild [skip ci]
nextstrain-bot May 12, 2026
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16 changes: 2 additions & 14 deletions data/community/itps/orov/L/refseq/pathogen.json
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Expand Up @@ -7,25 +7,13 @@
"attributes": {
"name": "orov/L/refseq",
"reference accession": "NC_005776.1",
"reference name": "Oropouche virus, L segment"
"reference name": "Oropouche virus, L segment",
"experimental": true
},
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
},
"placementMaskRanges": [
{
"begin": 0,
"end": 43
},
{
"begin": 6796,
"end": 6846
}
],
"deprecated": false,
"enabled": true,
"experimental": true,
"files": {
"changelog": "CHANGELOG.md",
"examples": "sequences.fasta",
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20 changes: 17 additions & 3 deletions data/community/itps/orov/L/refseq/tree.json
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Expand Up @@ -11,7 +11,7 @@
],
"maintainers": [
{
"name": "Instituto Todos pela Sa\u00fade",
"name": "Instituto Todos pela Saúde",
"url": "https://www.itps.org.br/"
}
],
Expand Down Expand Up @@ -85,7 +85,21 @@
"map",
"entropy",
"frequencies"
]
],
"extensions": {
"nextclade": {
"placement_mask_ranges": [
{
"begin": 0,
"end": 43
},
{
"begin": 6796,
"end": 6846
}
]
}
}
},
"tree": {
"name": "NODE_0000000",
Expand Down Expand Up @@ -10338,4 +10352,4 @@
"L": "MSQLLLNQYRNRILHCREPEIAKDIWRDLLNDRHNYFSREFCRAANLEYRNDVPAEDICAEVLDGYKARKVRFCTPDNYLLHDGKMYIIDFKVSVDDRSSRITREKYNEIFGEVFNPEGVDFEIVIIRLDPSNMTIHVDSRDFVNTIGPITLNISMQWFFDMKDFLFGKFRDDDKFHAIISQGEFTMTLPWIEEDTPELLTHPIYNEFMSSMPEAEQALFKEALEFKSFGAEKWNIFLKGVMSKYGEYYKEFTKGHAHSIFLTTGDYPKPDKDQISAGWREMVNRVSSERDMSNDINQEKPSMHFIWAKNDSNSNNNIQKLIKLSKSLQAMSGTGSYVNAFKSLGRLMDISSDVKKYESFCGKLKSLARSSIKKLDRKIEPIQIGTATVLWEQQFKLDTDVIKREDRIHLMKDYLGIGKHKSFSKKLNNDINTDKPKILNFNNDDIVRKCKDKYNQVIHNLSQINELDKIGNYLEHFSAKISACSVEMWDFIYNTTKTKYWQCINDYSTLMKNMLAVSQYNRHNTFRIVSCANNNVFGLVMPSSDIKTKKATLVYAIMALHNEEAEIAELGSLYSTFKTATGYISISKAFRLDKERCQRIVSSPGLFLMTSCLLFNGNKSLEFDKLLGFSFFTSISITKAMLSLTEPSRYMIMNSLAVSSHVREYISEKFSPYTKTSFSVVMTDLIKKGCYSAYEQRKKVQIRDIKLTDYDITQKGVDSKRDLKSIWFPGKVNLKEYLNQIYLPFYFNSKGLHEKHHVLIDLAKTVLEIEKEQRESLPEPWSEIPAKRLSLNVLIYSLQELNLDTSRHNFVRSRVENANNFNRSITTISTFTSSKSCIKIGDFEEEKREKLRMIQKKLAKDISKLTIANPAFLDEITNEHEIRHSTYEDLKQSIPDYTDYMSVKVFDRLYEKITTNEINDKETVKLILETMKKHKIFHFGFFNKGQKTAKDREIFLGEFEAKMCLYLVERIAKERCKLNPEEMISEPGDSKLRVLEKQSEDEIRYISNTIKTLGNAIENLQSGSLNWADICENKARGLKIEINADMSKWSAQDVLFKYFWLIVLDPILYPAERKRIIYFLCNYMQKRLIMPDELLTTILDQRVPYSNDIIGLMTNNYRSNTVEIKRNWLQGNLNYTSSYLHSCSMSVYKDIIREAAILLEGEALVNSMVHSDDNQTSICMVQNKLPDDNIIEFCIKIFEKICLTFGNQANMKKTYLTNFIKEFVSLFNIHGEPFSIYGRFLLTAVGDCAYLGPYEDLASRLSATQTAIKHGCPPSLAWVSIALNHWITHTTYNMLPGQNNDPLPFFPTNNRSEIPVEMCGILESDLSTIALTGLEAGNVTFLTNIARKLSSPILQRESIQDQYNSIEKWDLSKLSQIDILRLKMLRYISLDSSVTSDDGMGETSEMRSRSLLTPRKFTTSGSLNRLKSYKDFQDIIADEDKTNELFENFIRHPELLVTKGETFEEFVNTILFRYNSKKFKESLSIQNPAQLFIEQILFSNKPVIDYTSIHDKIFGLQDMPGIEELDTIIGRKTFVESYVQIVDDLSNLTLDINDVKTIFAFCLMNDPLLITSANNIIMSVKGHSQERIGQSACKMPEVRSLKLIHYSPAVVLRAYVRGPTNVPNVDIDELARDLSHLEDFIQSTKLRENMRERIEINEKRHLGRDFKFEIKELTRFYQVCYDYIKSTEHKVKVFILPYKVFTSIEFCGALTGNLINDKLWYITHYLKNIVSTTHKAQISSSPELELQIADEALRLVAHFADTFLASESRIQFLKKIIEEFTYKGIPVKHLYSKIKNSKLRVKFLGILLWLDDLTQNDLDKFDADKSDEKIIWNNWQVSRDMNTGPIDLMISGYSRQLRITGEDDKLIAAELQVTRLSEDLIYRHGQAMLNKPHGLKLEKMQPVTEMSKRLHYIVFQQRSRKRYFYSILPTQVIEDHNSRVESSRLSRDSKWVPVCPVAISKLYQQGRPILSKVRNLNMQTHSLSRIQVNVDEYAITRRAHFQKMPFFEGPSIPSGGMDLSELMKSTSLLSLNYDNIKNASLLDMSRVFKCNGSGDDQMAFEFLSDEILEQDVVEEIECNPIFSISYTKRGESNMTYKNAFHKALISECDKFEEAFDFLDMGFCSNENLSILEEIHWIISYLKTNQWSTELDNCIHMCMYRNGYDAEYHKFDIPSKFLKDPINRTINWTEVIEFILLIEDFQTKIEPWSSMKSHFCSKAHSVALECMKNEKRSLAEFVDKSKKTGKSKFDF*",
"nuc": "AGTAGTGTGCTCCTATTCCGAAACAAACAAAAACAATCTCAAAATGTCACAACTGTTGCTCAACCAATATCGGAATAGGATATTGCACTGCCGTGAACCTGAGATAGCAAAGGATATATGGCGAGATCTATTAAATGATCGACACAATTACTTTTCTCGGGAATTTTGCAGAGCTGCAAATCTTGAGTACAGAAATGATGTTCCTGCTGAGGATATTTGTGCTGAAGTTCTTGATGGTTATAAAGCAAGGAAAGTTCGCTTTTGTACACCTGATAATTACTTACTACATGATGGAAAGATGTATATAATAGACTTCAAAGTGTCTGTAGACGACCGATCTTCTAGAATCACAAGGGAGAAATATAATGAGATTTTTGGAGAGGTATTCAATCCAGAAGGTGTAGATTTTGAAATTGTTATTATTAGATTAGATCCTTCAAATATGACGATACATGTGGACTCTCGAGATTTCGTGAATACAATTGGGCCGATTACATTAAACATTAGTATGCAATGGTTTTTTGATATGAAAGACTTCTTGTTCGGGAAATTTCGGGATGATGATAAATTCCATGCTATAATAAGTCAAGGAGAATTCACAATGACATTGCCATGGATTGAAGAAGACACCCCAGAATTGCTTACTCATCCTATATACAATGAATTCATGAGTTCAATGCCAGAGGCAGAACAGGCCCTATTCAAGGAAGCATTGGAATTCAAATCATTTGGGGCAGAAAAATGGAATATCTTTTTGAAGGGGGTGATGTCAAAGTATGGTGAATATTATAAAGAATTTACTAAAGGACATGCTCATTCTATATTTCTGACAACAGGGGACTACCCCAAGCCAGACAAAGACCAAATTTCAGCAGGTTGGAGAGAAATGGTAAACAGAGTAAGCTCTGAACGTGACATGTCAAATGACATAAATCAGGAAAAACCAAGCATGCATTTTATATGGGCAAAGAATGATTCAAATAGCAACAATAATATACAAAAGCTAATCAAACTATCTAAATCACTGCAAGCTATGAGCGGGACAGGGAGCTATGTAAATGCTTTCAAGTCATTAGGGAGATTAATGGATATATCATCAGATGTTAAAAAATATGAATCATTTTGTGGGAAATTGAAATCTCTGGCAAGGTCTAGTATAAAAAAACTTGACAGGAAAATAGAGCCAATACAAATTGGGACTGCAACTGTCTTATGGGAACAGCAATTTAAACTAGATACAGATGTTATAAAAAGAGAAGACAGAATACATTTAATGAAAGATTATCTTGGGATCGGTAAGCACAAATCATTTTCAAAGAAATTAAACAACGACATAAATACTGATAAGCCTAAAATATTAAATTTCAACAATGATGATATAGTCAGGAAATGCAAAGATAAATATAATCAAGTCATACATAACCTATCCCAAATCAATGAATTAGATAAGATTGGAAACTACCTAGAGCACTTTTCAGCTAAAATTAGTGCCTGCAGTGTAGAAATGTGGGATTTTATATATAATACAACCAAAACTAAATACTGGCAATGCATCAATGACTATTCCACCCTAATGAAAAACATGTTAGCTGTCTCTCAATATAATAGACACAATACGTTTAGAATTGTCTCATGTGCAAACAATAATGTATTTGGTCTAGTAATGCCAAGCTCAGATATAAAGACAAAAAAAGCAACTTTAGTCTATGCAATAATGGCTCTCCATAATGAGGAGGCAGAAATAGCAGAACTTGGCTCACTCTACTCAACTTTTAAGACAGCAACAGGATATATTTCAATATCAAAGGCTTTTAGGCTGGATAAAGAAAGATGCCAACGCATAGTATCCTCTCCAGGCTTGTTCCTCATGACAAGCTGCCTATTATTCAACGGTAACAAGAGTTTAGAATTTGATAAATTACTAGGATTTTCATTTTTTACGTCAATATCAATTACGAAAGCTATGCTCTCCCTTACTGAGCCTTCACGTTATATGATCATGAACTCGTTAGCAGTTTCCAGCCATGTAAGAGAGTATATATCTGAAAAATTCTCCCCTTATACAAAAACATCATTTTCTGTGGTAATGACAGACTTAATCAAGAAGGGTTGCTATTCAGCATATGAACAGAGAAAAAAAGTACAAATAAGAGACATAAAATTAACAGATTATGATATAACACAAAAGGGAGTGGATTCCAAAAGAGATCTTAAATCTATTTGGTTCCCAGGAAAGGTAAACCTGAAAGAATATTTAAACCAAATTTATCTACCATTTTATTTTAACTCTAAAGGATTACATGAAAAACATCATGTCTTGATAGATTTGGCTAAAACAGTACTAGAAATCGAAAAAGAGCAAAGGGAGTCATTACCTGAGCCATGGTCAGAGATACCTGCTAAGCGACTGTCACTTAATGTTTTAATTTACTCATTGCAGGAACTGAATTTAGATACTTCAAGACATAATTTTGTAAGAAGCCGGGTGGAAAACGCAAATAATTTCAACAGATCTATAACGACAATATCTACTTTTACCAGCTCAAAATCATGCATTAAGATTGGTGATTTTGAAGAAGAAAAAAGAGAAAAACTAAGAATGATACAAAAGAAACTTGCAAAGGATATTTCTAAATTAACCATAGCCAACCCAGCATTCTTAGATGAGATCACAAACGAACATGAGATAAGGCATTCAACTTATGAGGACTTAAAACAATCTATCCCAGATTACACAGATTATATGTCTGTGAAAGTTTTTGACAGATTGTACGAGAAGATTACTACCAATGAAATAAATGATAAGGAAACAGTCAAGCTGATTCTAGAGACCATGAAAAAACATAAAATATTTCATTTTGGATTCTTCAATAAAGGACAAAAAACAGCCAAAGATAGAGAAATATTTTTAGGTGAATTTGAAGCAAAAATGTGTCTGTACCTTGTCGAAAGAATAGCTAAAGAGAGGTGCAAATTAAACCCTGAAGAAATGATAAGTGAACCAGGCGACTCGAAACTAAGGGTATTAGAGAAGCAATCAGAAGACGAAATCAGGTATATTAGCAATACAATAAAGACATTAGGGAATGCCATAGAGAACTTGCAATCTGGATCTTTAAATTGGGCAGATATATGCGAAAACAAAGCAAGAGGACTTAAGATAGAAATAAATGCTGATATGTCCAAATGGAGTGCCCAAGATGTACTTTTTAAATATTTTTGGTTGATAGTGCTTGATCCCATCTTATATCCTGCTGAGAGGAAAAGGATAATTTATTTCCTCTGTAATTATATGCAGAAAAGGCTTATAATGCCCGATGAATTGCTCACTACTATATTGGATCAAAGAGTTCCTTATTCAAATGACATAATTGGATTAATGACAAACAATTATAGGTCTAATACAGTAGAAATAAAGCGTAACTGGCTTCAAGGCAACTTAAATTATACAAGCAGTTACTTACACAGCTGTAGTATGTCTGTGTACAAAGATATAATAAGAGAAGCAGCAATATTATTAGAAGGAGAAGCCCTTGTGAACTCAATGGTACATTCTGATGATAATCAAACATCTATATGTATGGTGCAGAATAAATTACCAGATGACAATATAATTGAATTTTGCATTAAGATATTCGAGAAGATATGCTTAACTTTTGGCAATCAGGCAAATATGAAGAAGACATATCTAACTAACTTCATCAAAGAGTTTGTTTCTTTATTTAATATACATGGAGAACCATTTTCTATATATGGGAGATTTCTACTCACAGCAGTAGGAGACTGTGCCTATCTAGGGCCTTATGAAGATTTAGCAAGTAGGCTATCTGCAACACAAACTGCTATAAAGCATGGTTGCCCACCATCACTTGCATGGGTATCTATCGCTCTAAATCACTGGATAACCCACACTACATATAATATGTTGCCTGGCCAAAATAATGACCCGTTACCATTCTTCCCTACTAACAATAGAAGTGAAATACCAGTAGAGATGTGCGGAATACTAGAAAGTGATTTATCAACAATTGCACTAACTGGTTTAGAAGCAGGGAATGTCACGTTTCTAACAAATATAGCAAGGAAGTTATCATCCCCAATCTTACAAAGAGAAAGTATTCAAGATCAATACAATTCTATAGAAAAGTGGGATCTGAGCAAATTATCACAGATCGACATTCTAAGGCTTAAAATGCTCAGGTATATATCTCTTGATAGTTCAGTCACATCTGATGATGGTATGGGGGAGACTAGTGAAATGAGATCTCGATCACTTTTAACACCTCGTAAATTCACAACAAGTGGGTCACTTAATAGGTTGAAATCATATAAAGACTTTCAAGATATAATAGCAGATGAGGACAAGACAAACGAACTATTTGAGAATTTCATTAGACACCCAGAGTTACTGGTTACAAAAGGCGAAACATTTGAAGAATTTGTTAATACGATATTATTTAGGTACAATTCAAAGAAATTCAAAGAATCTTTGTCAATACAAAACCCAGCACAGCTTTTTATTGAGCAAATATTATTTTCCAATAAACCAGTAATTGACTACACTAGCATACATGACAAGATTTTTGGATTACAAGACATGCCAGGAATTGAAGAACTAGATACAATTATAGGTCGCAAAACATTTGTTGAGAGTTATGTTCAAATCGTAGATGACTTAAGCAATTTAACATTGGATATAAACGATGTCAAGACTATATTTGCCTTTTGTCTTATGAATGACCCACTACTGATCACATCTGCTAACAATATAATAATGTCTGTTAAGGGACATAGTCAAGAAAGAATAGGTCAATCAGCATGCAAAATGCCAGAGGTCCGAAGTCTAAAACTCATACATTATTCACCAGCAGTTGTTTTGAGAGCCTATGTGAGAGGGCCAACAAATGTACCGAATGTAGATATAGATGAACTTGCAAGGGATCTATCTCATTTAGAAGACTTCATACAAAGTACAAAACTCAGAGAAAATATGAGAGAGAGAATAGAAATAAATGAGAAGCGGCACTTAGGAAGGGATTTCAAATTTGAAATCAAAGAACTAACTAGATTTTACCAAGTGTGTTATGATTACATAAAGTCTACAGAACATAAAGTCAAGGTATTCATATTGCCATACAAAGTTTTCACATCAATAGAATTCTGCGGGGCACTGACAGGTAACTTGATAAATGACAAATTATGGTACATAACGCATTATCTGAAAAATATAGTGTCTACTACACATAAGGCACAAATTTCTTCTTCACCTGAATTGGAATTGCAAATTGCTGATGAGGCACTAAGACTAGTAGCACATTTTGCTGATACTTTCTTGGCATCAGAATCAAGAATACAATTTCTGAAGAAAATTATTGAAGAATTCACATACAAAGGGATACCTGTAAAACATTTATACTCAAAAATAAAGAACTCCAAGTTGAGGGTTAAATTTCTAGGGATTCTTTTATGGTTAGATGATCTAACACAGAATGATCTGGATAAATTTGATGCAGATAAATCAGATGAAAAGATTATATGGAATAACTGGCAAGTGTCAAGAGATATGAATACTGGACCAATAGACTTAATGATAAGCGGTTACTCTAGACAGCTGCGGATCACTGGGGAAGATGACAAATTGATTGCTGCTGAATTGCAGGTTACTAGATTGTCAGAAGATTTAATTTATAGACACGGTCAGGCAATGTTGAATAAGCCACACGGCTTAAAGCTTGAAAAAATGCAACCTGTGACTGAGATGTCTAAACGATTACATTATATCGTTTTCCAGCAAAGATCACGGAAACGATACTTCTATTCTATATTACCCACCCAAGTAATTGAGGACCATAATTCTAGAGTTGAATCATCTAGGCTAAGCAGAGATTCAAAATGGGTTCCTGTATGCCCTGTTGCAATATCAAAACTCTACCAACAAGGACGGCCTATACTTTCCAAAGTTAGAAATCTGAATATGCAGACTCATTCGCTTTCCAGAATACAAGTTAATGTAGATGAATATGCCATCACGAGAAGAGCACATTTTCAGAAAATGCCTTTCTTCGAAGGACCATCAATCCCTTCTGGTGGTATGGATTTGTCTGAGTTGATGAAATCTACATCCCTATTAAGCTTGAATTATGATAACATAAAAAATGCATCCTTATTGGACATGTCTAGGGTATTTAAGTGCAATGGCAGTGGAGATGACCAAATGGCTTTCGAATTTCTATCGGACGAAATTTTGGAGCAAGATGTAGTTGAAGAAATAGAATGCAACCCTATATTTTCTATTAGTTATACAAAAAGAGGAGAATCCAATATGACTTATAAAAATGCTTTCCACAAAGCCTTAATCTCAGAATGTGACAAATTTGAAGAAGCATTTGACTTCCTCGACATGGGATTTTGCTCGAATGAAAATCTTAGTATTCTGGAGGAAATACATTGGATAATCAGTTATTTAAAAACAAATCAATGGTCTACGGAACTAGACAATTGTATTCACATGTGCATGTACAGGAATGGATATGATGCAGAATATCATAAATTTGATATACCCTCTAAATTCCTCAAAGACCCAATAAACCGAACAATAAATTGGACTGAAGTCATTGAATTTATATTATTAATTGAAGATTTCCAAACAAAAATTGAGCCATGGTCTAGTATGAAGTCACACTTCTGTTCAAAAGCACACAGTGTAGCACTAGAGTGTATGAAAAATGAGAAAAGATCATTGGCAGAATTTGTAGACAAAAGTAAGAAAACTGGCAAATCCAAATTTGACTTCTAAGGTATACACATGTAAAAGTAGTGTTTGTTTCTAAATAGGAGCACACTACT"
}
}
}
16 changes: 2 additions & 14 deletions data/community/itps/orov/L/tefe/pathogen.json
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Original file line number Diff line number Diff line change
Expand Up @@ -6,25 +6,13 @@
"attributes": {
"name": "orov/L/tefe",
"reference accession": "PP154172.1",
"reference name": "Oropouche virus ILMD_TF29 (tefe), L segment"
"reference name": "Oropouche virus ILMD_TF29 (tefe), L segment",
"experimental": true
},
"compatibility": {
"cli": "3.0.0-alpha.0",
"web": "3.0.0-alpha.0"
},
"placementMaskRanges": [
{
"begin": 0,
"end": 35
},
{
"begin": 6794,
"end": 6814
}
],
"deprecated": false,
"enabled": true,
"experimental": true,
"files": {
"changelog": "CHANGELOG.md",
"examples": "sequences.fasta",
Expand Down
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