{"id":"https://openalex.org/W1992312974","doi":"https://doi.org/10.1093/nar/gkq298","title":"SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction","display_name":"SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction","publication_year":2010,"publication_date":"2010-04-29","ids":{"openalex":"https://openalex.org/W1992312974","doi":"https://doi.org/10.1093/nar/gkq298","mag":"1992312974","pmid":"https://pubmed.ncbi.nlm.nih.gov/20430824"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq298","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq298","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W29/3827199/gkq298.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W29/3827199/gkq298.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066147479","display_name":"Raffi Hagopian","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Hagopian","raw_affiliation_strings":["Department of Bioengineering, University of California, Berkeley, CA 94720, USA","Department of Bioengineering, University of California Berkeley, CA 94720, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, University of California Berkeley, CA 94720, USA#TAB#","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087858354","display_name":"Janelle Davidson","orcid":null},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. R. Davidson","raw_affiliation_strings":["Department of Bioengineering, 2 QB3 Institute and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, 2 QB3 Institute and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034710937","display_name":"Ruchira S. Datta","orcid":"https://orcid.org/0000-0003-2130-5818"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. S. Datta","raw_affiliation_strings":["Department of Bioengineering, 2 QB3 Institute and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, 2 QB3 Institute and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036130616","display_name":"Bushra Samad","orcid":"https://orcid.org/0000-0002-2893-0897"},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Samad","raw_affiliation_strings":["Department of Bioengineering, 2 QB3 Institute and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, 2 QB3 Institute and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109975790","display_name":"G. R. Jarvis","orcid":null},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"G. R. Jarvis","raw_affiliation_strings":["Department of Bioengineering, 2 QB3 Institute and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, 2 QB3 Institute and 3 Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107849607","display_name":"Kimmen Sj\u00f6lander","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. Sjolander","raw_affiliation_strings":["Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, 2QB3 Institute and 3Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.2822,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.87631264,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"Web Server","first_page":"W29","last_page":"W34"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9799000024795532,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9765999913215637,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.8102633357048035},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.7498031854629517},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6912877559661865},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.673292338848114},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6358107328414917},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6257742643356323},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.6077008843421936},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.580393373966217},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5709860324859619},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4561845362186432},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45005863904953003},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4156014323234558},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3501719832420349},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33643582463264465},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.13741406798362732},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11568596959114075},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.10253581404685974},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09825161099433899}],"concepts":[{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.8102633357048035},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.7498031854629517},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6912877559661865},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.673292338848114},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6358107328414917},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6257742643356323},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.6077008843421936},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.580393373966217},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5709860324859619},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4561845362186432},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45005863904953003},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4156014323234558},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3501719832420349},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33643582463264465},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.13741406798362732},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11568596959114075},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.10253581404685974},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09825161099433899},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkq298","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq298","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W29/3827199/gkq298.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:20430824","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20430824","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:ark:/13030/qt4186t696","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org/ark:/13030/qt4186t696","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/4186t696","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic acids research, vol 38, iss Web Server issue","raw_type":"article"},{"id":"pmh:oai:open-archive.highwire.org:nar:38/suppl_2/W29","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/38/suppl_2/W29","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:2896197","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkq298","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkq298","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq298","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W29/3827199/gkq298.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W1992312974.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1508885706","https://openalex.org/W1965309444","https://openalex.org/W1974160388","https://openalex.org/W2007668764","https://openalex.org/W2009406556","https://openalex.org/W2016279534","https://openalex.org/W2027542060","https://openalex.org/W2055033601","https://openalex.org/W2102122585","https://openalex.org/W2102524821","https://openalex.org/W2110534451","https://openalex.org/W2117752525","https://openalex.org/W2118488195","https://openalex.org/W2119362018","https://openalex.org/W2119801041","https://openalex.org/W2120772351","https://openalex.org/W2124815061","https://openalex.org/W2132395520","https://openalex.org/W2132926880","https://openalex.org/W2137015675","https://openalex.org/W2140872496","https://openalex.org/W2142529984","https://openalex.org/W2144362290","https://openalex.org/W2144965592","https://openalex.org/W2159500193","https://openalex.org/W2162566191","https://openalex.org/W2164652663","https://openalex.org/W2168508791"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2378969149","https://openalex.org/W2133116680","https://openalex.org/W2135668486","https://openalex.org/W2105364679","https://openalex.org/W1996516710","https://openalex.org/W2167269469"],"abstract_inverted_index":{"We":[0],"present":[1],"the":[2,55,62,78,82,86,104,130],"jump-start":[3,71],"simultaneous":[4,17],"alignment":[5,117],"and":[6,25,40,45,65,91,129],"tree":[7,44],"construction":[8],"using":[9,123],"hidden":[10],"Markov":[11],"models":[12],"(SATCHMO-JS)":[13],"web":[14],"server":[15,29],"for":[16,149],"estimation":[18],"of":[19,35,61,85,98],"protein":[20],"multiple":[21],"sequence":[22],"alignments":[23],"(MSAs)":[24],"phylogenetic":[26,43,79],"trees.":[27],"The":[28,134,141],"takes":[30],"as":[31],"input":[32],"a":[33,42,67,74,95,112],"set":[34],"sequences":[36],"in":[37,77,116,144],"FASTA":[38],"format,":[39],"outputs":[41],"MSA;":[46],"these":[47,145],"can":[48],"be":[49],"viewed":[50],"online":[51],"or":[52],"downloaded":[53],"from":[54,103],"website.":[56],"SATCHMO-JS":[57,110,135],"is":[58,137],"an":[59],"extension":[60],"SATCHMO":[63,72,132],"algorithm,":[64],"employs":[66],"divide-and-conquer":[68],"strategy":[69],"to":[70],"at":[73,139,151],"higher":[75],"point":[76],"tree,":[80],"reducing":[81],"computational":[83],"complexity":[84],"progressive":[87],"all-versus-all":[88],"HMM-HMM":[89],"scoring":[90],"alignment.":[92],"Results":[93],"on":[94],"benchmark":[96,106],"dataset":[97,107],"983":[99],"structurally":[100],"aligned":[101],"pairs":[102],"PREFAB":[105],"show":[108],"that":[109],"provides":[111],"statistically":[113],"significant":[114],"improvement":[115],"accuracy":[118],"over":[119],"MUSCLE,":[120],"Multiple":[121],"Alignment":[122],"Fast":[124],"Fourier":[125],"Transform":[126],"(MAFFT),":[127],"ClustalW":[128],"original":[131],"algorithm.":[133],"webserver":[136],"available":[138,148],"http://phylogenomics.berkeley.edu/satchmo-js.":[140],"datasets":[142],"used":[143],"experiments":[146],"are":[147],"download":[150],"http://phylogenomics.berkeley.edu/satchmo-js/supplementary/.":[152]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
