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Use accession column as ID column
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kimandrews committed Mar 5, 2024
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4 changes: 4 additions & 0 deletions phylogenetic/defaults/config.yaml
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Expand Up @@ -8,9 +8,13 @@ filter:
sequences_per_group: 20
min_date: 1950
min_length: 5000
strain_id: "accession"
refine:
coalescent: "opt"
date_inference: "marginal"
clock_filter_iqd: 4
strain_id: "accession"
ancestral:
inference: "joint"
export:
strain_id: "accession"
4 changes: 2 additions & 2 deletions phylogenetic/defaults/dropped_strains.txt
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temara.MOR/24.03
Mvs/Toulon.FRA/08.07
HM562901.1 # temara.MOR/24.03
HM562900.1 # Mvs/Toulon.FRA/08.07
42 changes: 21 additions & 21 deletions phylogenetic/example_data/metadata.tsv
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strain virus accession date region country division city db segment authors url title journal paper_url
Arizona.USA/11.08/2 measles JN635406 2008-03-11 North America Usa Usa Usa genbank genome Kirkness et al https://www.ncbi.nlm.nih.gov/nuccore/JN635406 Direct Submission Submitted (30-AUG-2011) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/
London.GBR/3.14/2/B3 measles KT732220 2014-01-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732220 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
London.GBR/3.14/3/B3 measles KT732221 2014-01-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732221 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
Roraima.BRA/31.18/D8 measles MK161348 2018-08-04 South America Brazil Brazil Brazil genbank genome Meneses et al https://www.ncbi.nlm.nih.gov/nuccore/MK161348 Complete genome of a Measles virus from Roraima state, Brazil bioRxivorg (2018) In press https://www.ncbi.nlm.nih.gov/pubmed/
Ancona.ITA/45.17/1/D8 measles MH173047 2017-11-XX Europe Italy Italy Italy genbank genome Marinelli et al https://www.ncbi.nlm.nih.gov/nuccore/MH173047 Direct Submission Submitted (06-APR-2018) Ao Ospedali Riuniti Di Ancona, Virologia, Via Conca, 71, Ancona 60020, Italy https://www.ncbi.nlm.nih.gov/pubmed/
Zhejiang.CHN/12.09/1/H1 measles KJ755980 2009-03-18 China China China China genbank genome Jin et al https://www.ncbi.nlm.nih.gov/nuccore/KJ755980 Evolutionary history of the endemic strains of Chinese Measles virus Unpublished https://www.ncbi.nlm.nih.gov/pubmed/
Shanghai-191 measles FJ416067 ? China China China China genbank genome Zhang et al https://www.ncbi.nlm.nih.gov/nuccore/FJ416067 Genetic characterization of Chinese measles vaccines by analysis of complete genomic sequences J. Med. Virol. 81 (8), 1477-1483 (2009) https://www.ncbi.nlm.nih.gov/pubmed/19551837
New_Jersey.USA/45.05 measles JN635408 2005-11-05 North America Usa Usa Usa genbank genome Kirkness et al https://www.ncbi.nlm.nih.gov/nuccore/JN635408 Direct Submission Submitted (30-AUG-2011) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA https://www.ncbi.nlm.nih.gov/pubmed/
Gambia/1993 measles EF565859 1993-XX-XX Africa Gambia Gambia Gambia genbank genome Druelle et al https://www.ncbi.nlm.nih.gov/nuccore/EF565859 Wild type measles virus attenuation independent of type I IFN Virol. J. 5, 22 (2008) https://www.ncbi.nlm.nih.gov/pubmed/18241351
London.GBR/3.14/B3 measles KT732219 2014-01-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732219 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
London.GBR/4.14/2/B3 measles KT732223 2014-01-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732223 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
T11 measles AB481088 1989-XX-XX Japan Korea Japan Japan Japan genbank genome Okada et al https://www.ncbi.nlm.nih.gov/nuccore/AB481088 Previously unrecognized amino acid substitutions in the hemagglutinin and fusion proteins of measles virus modulate cell-cell fusion, hemadsorption, virus growth, and penetration rate J. Virol. 83 (17), 8713-8721 (2009) https://www.ncbi.nlm.nih.gov/pubmed/19553316
Paris.FRA/18.11/D4 measles MF449469 2011-05-03 Europe France France France genbank genome Mura et al https://www.ncbi.nlm.nih.gov/nuccore/MF449469 Non-encapsidated 5' copy-back defective-interfering genomes produced by recombinant measles viruses are recognized by RIG-I and LGP2 but not MDA5 J. Virol. (2017) In press https://www.ncbi.nlm.nih.gov/pubmed/28768856
Teeside.GBR/16.13/6/D8 measles KT732253 2013-04-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732253 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
Zhejiang.CHN/12.08/1/H1 measles KJ755979 2008-03-20 China China China China genbank genome Jin et al https://www.ncbi.nlm.nih.gov/nuccore/KJ755979 Evolutionary history of the endemic strains of Chinese Measles virus Unpublished https://www.ncbi.nlm.nih.gov/pubmed/
London.GBR/20.11/2/D4 measles KT732226 2011-05-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732226 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
Derby.GBR/47.12/D8 measles KT732241 2012-11-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732241 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
Swansea.GBR/16.13/5/D8 measles KT732255 2013-04-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732255 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
9301V measles AB012949 ? ? ? ? ? genbank genome Takeda et al https://www.ncbi.nlm.nih.gov/nuccore/AB012949 Measles virus attenuation associated with transcriptional impediment and a few amino acid changes in the polymerase and accessory proteins J. Virol. 72 (11), 8690-8696 (1998) https://www.ncbi.nlm.nih.gov/pubmed/9765410
Swansea.GBR/16.13/2/D8 measles KT732251 2013-04-XX Europe United Kingdom ? ? genbank genome Penedos et al https://www.ncbi.nlm.nih.gov/nuccore/KT732251 Assessment of the Utility of Whole Genome Sequencing of Measles Virus in the Characterisation of Outbreaks PLoS ONE 10 (11), E0143081 (2015) https://www.ncbi.nlm.nih.gov/pubmed/26569100
accession strain virus_name date region country division location length host date_released date_updated sra_accessions authors abbr_authors institution
MK161348.1 D8 2018-08-04 South America Brazil Boa Vista Roraima State 15894 Homo sapiens 2018-11-20 2019-04-10 Meneses,C.A.,Nascimento,V.A.,Souza,V.C.,Maito,R.M.,Gomes,M.A.,Cunha,C.R.,Antony,I.A.,Silva,M.E.,Campos,D.P.,Corado,A.L.,Pessoa,K.P.,Monteiro,D.C.,Okumoto,O.,Cunha,M.C.,Pacheco,F.C.,Naveca,F.G.,Corado,A.G. Meneses et al Instituto Leonidas e Maria Deane - Fiocruz Amazonia, Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia
MH173047.1 D8 2017-11-XX Europe Italy 15872 Homo sapiens 2018-06-06 2018-06-06 Marinelli,K.,Caucci,S.,Vincenzi,C.,Ferreri,M.,Magurano,F.,Bagnarelli,P.,Menzo,S. Marinelli et al Virologia, Ao Ospedali Riuniti Di Ancona
MF449469.1 G2V D4 2011-05-03 Europe France 15894 Homo sapiens 2017-08-28 2017-08-28 Mura,M.,Combredet,C.,Najburg,V.,Sanchez David,R.Y.,Tangy,F.,Komarova,A.V.,Sanchez-David,R.Y.,Komarova,A. Mura et al Institut Pasteur, Virology
KT732255.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732253.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732251.1 D8 2013-04-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732241.1 D8 2012-11-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732226.1 D4 2011-05-XX Europe United Kingdom 15684 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732223.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732221.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732220.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KT732219.1 B3 2014-01-XX Europe United Kingdom 15678 Homo sapiens 2015-09-20 2015-12-03 Penedos,A.R.,Myers,R.,Hadef,B.,Aladin,F.,Brown,K.E.,Penedos,A. Penedos et al Public Health England, Virus Reference Department, National Infection Service
KJ755980.1 H1 2009-03-18 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology
KJ755979.1 H1 2008-03-20 Asia China 15894 Homo sapiens 2016-05-02 2016-05-02 Jin,Q.,Xu,C.,Li,H.,Zhong,S.,Zheng,B.,Lu,Y. Jin et al Centre for Disease Control and Prevention of Zhejiang Province (ZJ CDC), Institute of Microbiology
JN635408.1 2005-11-05 North America USA New Jersey 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute
JN635406.1 2008-03-11 North America USA Arizona 15894 Homo sapiens 2011-09-29 2012-01-26 Kirkness,E.F.,Halpin,R.,Bera,J.,Fedorova,N.,Overton,L.,Stockwell,T.,Amedeo,P.,Bishop,B.,Chen,H.,Edworthy,P.,Gupta,N.,Katzel,D.,Li,K.,Schobel,S.,Shrivastava,S.,Thovarai,V.,Wang,S.,Bankamp,B.,Byrd,L.,Bellini,W.,Rota,P. Kirkness et al J. Craig Venter Institute
FJ416067.1 15894 2009-05-21 2009-11-05 Zhang,Y.,Zhou,J.,Bellini,W.J.,Xu,W.,Rota,P.A.,Bamkamp,B. Zhang et al National Institute for Viral Disease Control and Prevention, China Centers for Disease Control and Prevention, WHO WPRO Regional Reference Measles Lab
EF565859.1 G954-PBL 1993-XX-XX Africa 6552 2008-04-02 2008-04-02 Druelle,J.,Sellin,C.I.,Waku-Kouomou,D.,Horvat,B.,Wild,F.T.,Sellin,C.,Wild,T. Druelle et al Inserm U404, Immunite et Vaccination
AB481088.1 1989-XX-XX Asia Japan 15894 2009-08-14 2009-08-14 Okada,H.,Itoh,M.,Nagata,K.,Takeuchi,K.,Ito,M. Okada et al Graduate School of Comprehensive Human Sciences; Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575
AB012949.1 9301V 15894 Homo sapiens 1998-10-19 2008-12-04 Takeda,M.,Kato,A.,Kobune,F.,Sakata,H.,Li,Y.,Shioda,T.,Sakai,Y.,Asakawa,M.,Nagai,Y. Takeda et al University of Tokyo, Viral Infection; Shirokanedai 4-6-1, Minato-ku, Tokyo 108
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