{"id":"https://openalex.org/W3173893761","doi":"https://doi.org/10.1186/s12859-021-04274-6","title":"Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life","display_name":"Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life","publication_year":2021,"publication_date":"2021-06-29","ids":{"openalex":"https://openalex.org/W3173893761","doi":"https://doi.org/10.1186/s12859-021-04274-6","mag":"3173893761","pmid":"https://pubmed.ncbi.nlm.nih.gov/34187366"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04274-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04274-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04274-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"software-paper","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04274-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052346049","display_name":"Luna L. S\u00e1nchez\u2010Reyes","orcid":"https://orcid.org/0000-0001-7668-2528"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Luna L. S\u00e1nchez-Reyes","raw_affiliation_strings":["School of Natural Sciences, University of California, Merced, USA. lsanchezreyes2@ucmerced.edu","School of Natural Sciences, University of California, Merced, USA"],"raw_orcid":"https://orcid.org/0000-0001-7668-2528","affiliations":[{"raw_affiliation_string":"School of Natural Sciences, University of California, Merced, USA. lsanchezreyes2@ucmerced.edu","institution_ids":["https://openalex.org/I156087764"]},{"raw_affiliation_string":"School of Natural Sciences, University of California, Merced, USA","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053329269","display_name":"Martha Kandziora","orcid":"https://orcid.org/0000-0002-1197-6207"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]},{"id":"https://openalex.org/I21250087","display_name":"Charles University","ror":"https://ror.org/024d6js02","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21250087"]}],"countries":["CZ","US"],"is_corresponding":false,"raw_author_name":"Martha Kandziora","raw_affiliation_strings":["Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic","School of Natural Sciences, University of California, Merced, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic","institution_ids":["https://openalex.org/I21250087"]},{"raw_affiliation_string":"School of Natural Sciences, University of California, Merced, USA","institution_ids":["https://openalex.org/I156087764"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031118780","display_name":"Emily Jane McTavish","orcid":"https://orcid.org/0000-0001-9766-5727"},"institutions":[{"id":"https://openalex.org/I156087764","display_name":"University of California, Merced","ror":"https://ror.org/00d9ah105","country_code":"US","type":"education","lineage":["https://openalex.org/I156087764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emily Jane McTavish","raw_affiliation_strings":["School of Natural Sciences, University of California, Merced, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Natural Sciences, University of California, Merced, USA","institution_ids":["https://openalex.org/I156087764"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5052346049"],"corresponding_institution_ids":["https://openalex.org/I156087764"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":null,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"1","first_page":"355","last_page":"355"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8730000257492065,"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":0.8730000257492065,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.026900000870227814,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10385","display_name":"Plant Diversity and Evolution","score":0.014399999752640724,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8333619832992554},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.656450092792511},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6341418027877808},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5431382656097412},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4888855516910553},{"id":"https://openalex.org/keywords/tree-of-life","display_name":"Tree of life (biology)","score":0.46893811225891113},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.44523367285728455},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44106048345565796},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.43018126487731934},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12399974465370178},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12171804904937744},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10829105973243713},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08438676595687866},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08095178008079529}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8333619832992554},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.656450092792511},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6341418027877808},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5431382656097412},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4888855516910553},{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.46893811225891113},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.44523367285728455},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44106048345565796},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.43018126487731934},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12399974465370178},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12171804904937744},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10829105973243713},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08438676595687866},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08095178008079529},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-021-04274-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04274-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04274-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34187366","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34187366","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8244228","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8244228","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e8436578a06543e6b16f79049b3be6e9","is_oa":true,"landing_page_url":"https://doaj.org/article/e8436578a06543e6b16f79049b3be6e9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-13 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04274-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04274-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04274-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.49000000953674316,"display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G5421047064","display_name":"MRI Acquisition: Multi-Environment Research Computer for Exploration and Discovery (MERCED) Cluster","funder_award_id":"1429783","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5639119659","display_name":null,"funder_award_id":"ACI-1429783","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5733108827","display_name":"Collaborative Research: ABI Development: Cultivating a sustainable Open Tree of Life","funder_award_id":"1759838","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7200776146","display_name":"Collaborative Research: ABI Development: Cultivating a sustainable Open Tree of Life","funder_award_id":"1759846","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3173893761.pdf","grobid_xml":"https://content.openalex.org/works/W3173893761.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1846926012","https://openalex.org/W1978854233","https://openalex.org/W2007569936","https://openalex.org/W2012196076","https://openalex.org/W2012284434","https://openalex.org/W2015930405","https://openalex.org/W2016279534","https://openalex.org/W2023028439","https://openalex.org/W2028309288","https://openalex.org/W2035415659","https://openalex.org/W2055043387","https://openalex.org/W2058938859","https://openalex.org/W2067432372","https://openalex.org/W2068187483","https://openalex.org/W2108867969","https://openalex.org/W2114850508","https://openalex.org/W2119744468","https://openalex.org/W2120663060","https://openalex.org/W2124511083","https://openalex.org/W2125230147","https://openalex.org/W2127803317","https://openalex.org/W2129594605","https://openalex.org/W2132926880","https://openalex.org/W2134038527","https://openalex.org/W2138042866","https://openalex.org/W2139736670","https://openalex.org/W2141052558","https://openalex.org/W2142678031","https://openalex.org/W2142678478","https://openalex.org/W2145252923","https://openalex.org/W2145562754","https://openalex.org/W2149737737","https://openalex.org/W2151375739","https://openalex.org/W2154809576","https://openalex.org/W2162050818","https://openalex.org/W2163023674","https://openalex.org/W2166152751","https://openalex.org/W2170041483","https://openalex.org/W2262686766","https://openalex.org/W2533812722","https://openalex.org/W2586648135","https://openalex.org/W2626273107","https://openalex.org/W2763775416","https://openalex.org/W2796277430","https://openalex.org/W2889206129","https://openalex.org/W2890156100","https://openalex.org/W2953087319","https://openalex.org/W2979671820","https://openalex.org/W2986514902","https://openalex.org/W2999309669","https://openalex.org/W3048090444","https://openalex.org/W3110696950","https://openalex.org/W3123097201","https://openalex.org/W4234303025","https://openalex.org/W4395210839","https://openalex.org/W6967346557"],"related_works":["https://openalex.org/W2763775416","https://openalex.org/W1977405831","https://openalex.org/W1979959438","https://openalex.org/W2174809885","https://openalex.org/W4210644918","https://openalex.org/W1474331782","https://openalex.org/W2883025420","https://openalex.org/W2088286307","https://openalex.org/W2057191541","https://openalex.org/W2949296710"],"abstract_inverted_index":{"BACKGROUND:":[0],"Phylogenies":[1],"are":[2,232],"a":[3,73,81,89,115,153,176],"key":[4],"part":[5],"of":[6,11,18,21,35,41,47,57,84,97,108,120,135,185,197],"research":[7],"in":[8,38],"many":[9],"areas":[10],"biology.":[12],"Tools":[13],"that":[14,70,93],"automate":[15],"some":[16],"parts":[17],"the":[19,33,39,95,132,150,195],"process":[20],"phylogenetic":[22,53,77,157,164,187],"reconstruction,":[23],"mainly":[24],"molecular":[25,180],"character":[26],"matrix":[27],"assembly,":[28],"have":[29],"been":[30],"developed":[31],"for":[32,60,117,201,207,228],"advantage":[34],"both":[36],"specialists":[37,170],"field":[40],"phylogenetics":[42],"and":[43,55,63,167,183,219,230],"non-specialists.":[44],"However,":[45],"interpretation":[46],"results,":[48],"comparison":[49,119,184],"with":[50,123,216],"previously":[51,109],"available":[52,162,233],"hypotheses,":[54],"selection":[56],"one":[58,69],"phylogeny":[59],"downstream":[61],"analyses":[62],"discussion":[64],"still":[65],"impose":[66],"difficulties":[67],"to":[68,105,138,155,178,205],"is":[71,88,220],"not":[72],"specialist":[74],"either":[75],"on":[76,80,160],"methods":[78],"or":[79],"particular":[82],"group":[83,169],"study.":[85],"RESULTS:":[86],"Physcraper":[87,192,212],"command-line":[90],"Python":[91],"program":[92,145],"automates":[94],"update":[96],"published":[98,110,121],"phylogenies":[99,122],"by":[100,127,149],"adding":[101],"public":[102],"DNA":[103],"sequences":[104],"underlying":[106],"alignments":[107],"phylogenies.":[111],"It":[112],"also":[113],"provides":[114],"framework":[116],"straightforward":[118],"their":[124],"updated":[125],"versions,":[126],"leveraging":[128],"upon":[129],"tools":[130],"from":[131],"Open":[133],"Tree":[134],"Life":[136],"project":[137],"link":[139],"taxonomic":[140,168],"information":[141],"across":[142],"databases.":[143],"The":[144,191],"can":[146,213],"be":[147,214],"used":[148,215],"nonspecialist,":[151],"as":[152,175],"tool":[154,177],"generate":[156],"hypotheses":[158,188],"based":[159],"publicly":[161],"expert":[163],"knowledge.":[165],"Phylogeneticists":[166],"will":[171],"find":[172],"it":[173],"useful":[174],"facilitate":[179],"dataset":[181],"gathering":[182],"alternative":[186],"(topologies).":[189],"CONCLUSION:":[190],"workflow":[193],"showcases":[194],"benefits":[196],"doing":[198],"open":[199],"science":[200],"phylogenetics,":[202],"encouraging":[203],"researchers":[204],"strive":[206],"better":[208],"scientific":[209],"sharing":[210],"practices.":[211],"any":[217],"OS":[218],"released":[221],"under":[222],"an":[223],"open-source":[224],"license.":[225],"Detailed":[226],"instructions":[227],"installation":[229],"usage":[231],"at":[234],"https://physcraper.readthedocs.io.":[235]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}