{"id":"https://openalex.org/W4290465972","doi":"https://doi.org/10.3390/software1030013","title":"AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories","display_name":"AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories","publication_year":2022,"publication_date":"2022-08-07","ids":{"openalex":"https://openalex.org/W4290465972","doi":"https://doi.org/10.3390/software1030013"},"language":"en","primary_location":{"id":"doi:10.3390/software1030013","is_oa":true,"landing_page_url":"https://doi.org/10.3390/software1030013","pdf_url":"https://www.mdpi.com/2674-113X/1/3/13/pdf?version=1662629280","source":{"id":"https://openalex.org/S4210183365","display_name":"Software","issn_l":"2674-113X","issn":["2674-113X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.mdpi.com/2674-113X/1/3/13/pdf?version=1662629280","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088739752","display_name":"David Schaller","orcid":"https://orcid.org/0000-0002-0025-3097"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"David Schaller","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, H\u00e4rtelstra\u00dfe 16\u201318, D-04107 Leipzig, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, H\u00e4rtelstra\u00dfe 16\u201318, D-04107 Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019719296","display_name":"Marc Hellmuth","orcid":"https://orcid.org/0000-0002-1620-5508"},"institutions":[{"id":"https://openalex.org/I161593684","display_name":"Stockholm University","ror":"https://ror.org/05f0yaq80","country_code":"SE","type":"education","lineage":["https://openalex.org/I161593684"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Marc Hellmuth","raw_affiliation_strings":["Department of Mathematics, Faculty of Science, Stockholm University, Roslagsv\u00e4gen 101, SE-10691 Stockholm, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Faculty of Science, Stockholm University, Roslagsv\u00e4gen 101, SE-10691 Stockholm, Sweden","institution_ids":["https://openalex.org/I161593684"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016104736","display_name":"Peter F. Stadler","orcid":"https://orcid.org/0000-0002-5016-5191"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]},{"id":"https://openalex.org/I36243813","display_name":"Universidad Nacional de Colombia","ror":"https://ror.org/059yx9a68","country_code":"CO","type":"education","lineage":["https://openalex.org/I36243813"]},{"id":"https://openalex.org/I4210091327","display_name":"Max Planck Institute for Mathematics in the Sciences","ror":"https://ror.org/00ez2he07","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210091327"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["AT","CO","DE","US"],"is_corresponding":false,"raw_author_name":"Peter F. Stadler","raw_affiliation_strings":["Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, H\u00e4rtelstra\u00dfe 16\u201318, D-04107 Leipzig, Germany","Department of Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria","Facultad de Ciencias, Universidad National de Colombia, Bogot\u00e1 111321, Colombia","Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, D-04103 Leipzig, Germany","Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, H\u00e4rtelstra\u00dfe 16\u201318, D-04107 Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria","institution_ids":["https://openalex.org/I129774422"]},{"raw_affiliation_string":"Facultad de Ciencias, Universidad National de Colombia, Bogot\u00e1 111321, Colombia","institution_ids":["https://openalex.org/I36243813"]},{"raw_affiliation_string":"Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, D-04103 Leipzig, Germany","institution_ids":["https://openalex.org/I4210091327"]},{"raw_affiliation_string":"Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA","institution_ids":["https://openalex.org/I1308548392"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5088739752"],"corresponding_institution_ids":["https://openalex.org/I926574661"],"apc_list":null,"apc_paid":{"value":1100,"currency":"EUR","value_usd":1186},"fwci":0.6076,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.64344814,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"1","issue":"3","first_page":"276","last_page":"298"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9896000027656555,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.9847999811172485,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/python","display_name":"Python (programming language)","score":0.9027701616287231},{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.7378792762756348},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6792890429496765},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4874277412891388},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37363699078559875},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3627324104309082},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3237497806549072},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2634853720664978},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2426375448703766},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13798460364341736},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.09828025102615356}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9027701616287231},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.7378792762756348},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6792890429496765},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4874277412891388},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37363699078559875},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3627324104309082},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3237497806549072},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2634853720664978},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2426375448703766},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13798460364341736},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.09828025102615356},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/software1030013","is_oa":true,"landing_page_url":"https://doi.org/10.3390/software1030013","pdf_url":"https://www.mdpi.com/2674-113X/1/3/13/pdf?version=1662629280","source":{"id":"https://openalex.org/S4210183365","display_name":"Software","issn_l":"2674-113X","issn":["2674-113X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Software","raw_type":"journal-article"},{"id":"pmh:oai:qucosa:de:qucosa:89003","is_oa":true,"landing_page_url":"https://ul.qucosa.de/id/qucosa%3A89003","pdf_url":null,"source":{"id":"https://openalex.org/S4377196312","display_name":"Qucosa (Saxon State and University Library Dresden)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I3132420320","host_organization_name":"SLUB Dresden","host_organization_lineage":["https://openalex.org/I3132420320"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"doc-type:Text"}],"best_oa_location":{"id":"doi:10.3390/software1030013","is_oa":true,"landing_page_url":"https://doi.org/10.3390/software1030013","pdf_url":"https://www.mdpi.com/2674-113X/1/3/13/pdf?version=1662629280","source":{"id":"https://openalex.org/S4210183365","display_name":"Software","issn_l":"2674-113X","issn":["2674-113X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5106512922","display_name":null,"funder_award_id":"Deutsche Forschungsgemeinschaft (DFG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6024419964","display_name":null,"funder_award_id":"Deutsche Forschungsgemeinschaft (DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6052429835","display_name":null,"funder_award_id":"(DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6871348130","display_name":null,"funder_award_id":"STA 850/51-2","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7751676430","display_name":null,"funder_award_id":"031A538B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8546080396","display_name":null,"funder_award_id":"031A538B","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8650825371","display_name":null,"funder_award_id":"STA 850/51-2","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4290465972.pdf","grobid_xml":"https://content.openalex.org/works/W4290465972.grobid-xml"},"referenced_works_count":98,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1593676244","https://openalex.org/W1844951369","https://openalex.org/W1910657848","https://openalex.org/W1967621400","https://openalex.org/W1979257831","https://openalex.org/W1990453950","https://openalex.org/W2005735443","https://openalex.org/W2007513570","https://openalex.org/W2017519756","https://openalex.org/W2019591778","https://openalex.org/W2020184108","https://openalex.org/W2024789434","https://openalex.org/W2038464976","https://openalex.org/W2041346050","https://openalex.org/W2041386815","https://openalex.org/W2044789834","https://openalex.org/W2044892321","https://openalex.org/W2045517599","https://openalex.org/W2050114121","https://openalex.org/W2062018285","https://openalex.org/W2065461553","https://openalex.org/W2074097929","https://openalex.org/W2078109763","https://openalex.org/W2090916413","https://openalex.org/W2099388422","https://openalex.org/W2099400989","https://openalex.org/W2099435674","https://openalex.org/W2100874222","https://openalex.org/W2114368970","https://openalex.org/W2115590956","https://openalex.org/W2116474217","https://openalex.org/W2117748102","https://openalex.org/W2119632499","https://openalex.org/W2121479060","https://openalex.org/W2122626634","https://openalex.org/W2125359798","https://openalex.org/W2125652789","https://openalex.org/W2127164334","https://openalex.org/W2129505888","https://openalex.org/W2129589314","https://openalex.org/W2139478957","https://openalex.org/W2143162227","https://openalex.org/W2143191932","https://openalex.org/W2143210482","https://openalex.org/W2151781607","https://openalex.org/W2152075687","https://openalex.org/W2152092111","https://openalex.org/W2152093282","https://openalex.org/W2155418451","https://openalex.org/W2157552136","https://openalex.org/W2159266221","https://openalex.org/W2161257056","https://openalex.org/W2163627198","https://openalex.org/W2170753094","https://openalex.org/W2170996473","https://openalex.org/W2180232428","https://openalex.org/W2186750819","https://openalex.org/W2269635123","https://openalex.org/W2277953252","https://openalex.org/W2286962642","https://openalex.org/W2316262244","https://openalex.org/W2586283250","https://openalex.org/W2765127695","https://openalex.org/W2766147358","https://openalex.org/W2766955181","https://openalex.org/W2779809586","https://openalex.org/W2790050774","https://openalex.org/W2792673049","https://openalex.org/W2801982793","https://openalex.org/W2914560485","https://openalex.org/W2950396894","https://openalex.org/W2963592740","https://openalex.org/W2972421638","https://openalex.org/W2977811825","https://openalex.org/W2999745586","https://openalex.org/W2999869862","https://openalex.org/W3000328796","https://openalex.org/W3003257820","https://openalex.org/W3012951261","https://openalex.org/W3017197234","https://openalex.org/W3129199054","https://openalex.org/W3165188249","https://openalex.org/W3180775633","https://openalex.org/W3210308821","https://openalex.org/W4200303939","https://openalex.org/W4214514396","https://openalex.org/W4229066198","https://openalex.org/W4229487902","https://openalex.org/W4230357098","https://openalex.org/W4253068584","https://openalex.org/W4283803957","https://openalex.org/W6638771720","https://openalex.org/W6678804063","https://openalex.org/W6696158138","https://openalex.org/W6776290371","https://openalex.org/W6805767352","https://openalex.org/W6948047203"],"related_works":["https://openalex.org/W2033001683","https://openalex.org/W2167094946","https://openalex.org/W4387460329","https://openalex.org/W2046457574","https://openalex.org/W1949458596","https://openalex.org/W4285059642","https://openalex.org/W3144677376","https://openalex.org/W32785519","https://openalex.org/W4382398022","https://openalex.org/W2160515792"],"abstract_inverted_index":{"AsymmeTree":[0,126,160],"is":[1,50,127,161],"a":[2,81],"flexible":[3],"and":[4,19,29,64,86,154],"easy-to-use":[5],"Python":[6,135],"package":[7],"for":[8,113,119],"the":[9,21,37,71,110,140,148,157],"simulation":[10],"of":[11,24,83,142],"gene":[12,25,34,72],"family":[13],"histories.":[14],"It":[15,146],"simulates":[16],"species":[17,38,114],"trees":[18],"considers":[20],"joint":[22],"action":[23],"duplication,":[26],"loss,":[27],"conversion,":[28],"horizontal":[30],"transfer":[31],"to":[32,130,138,150],"evolve":[33],"families":[35],"along":[36,70],"tree.":[39],"To":[40],"generate":[41],"realistic":[42],"scenarios,":[43],"evolution":[44],"rate":[45,62],"heterogeneity":[46],"from":[47,80],"various":[48],"sources":[49],"modeled.":[51],"Finally,":[52],"nucleotide":[53],"or":[54],"amino":[55],"acid":[56],"sequences":[57],"(optionally":[58],"with":[59],"indels,":[60],"among-site":[61],"heterogeneity,":[63],"invariant":[65],"sites)":[66],"can":[67,78,123],"be":[68,124,131],"simulated":[69,158],"phylogenies.":[73],"For":[74],"all":[75],"steps,":[76],"users":[77],"choose":[79],"spectrum":[82],"alternative":[84],"methods":[85],"parameters.":[87],"These":[88],"choices":[89],"include":[90],"most":[91],"options":[92],"that":[93,103],"are":[94,104],"commonly":[95],"used":[96],"in":[97,133],"comparable":[98],"tools":[99],"but":[100],"also":[101],"some":[102],"usually":[105],"not":[106],"found,":[107],"such":[108],"as":[109],"innovation":[111],"model":[112],"evolution.":[115],"While":[116],"output":[117],"files":[118],"each":[120],"individual":[121],"step":[122],"generated,":[125],"primarily":[128],"intended":[129],"integrated":[132],"complex":[134],"pipelines":[136],"designed":[137],"assess":[139],"performance":[141],"data":[143],"analysis":[144],"methods.":[145],"allows":[147],"user":[149],"interact":[151],"with,":[152],"analyze,":[153],"possibly":[155],"manipulate":[156],"scenarios.":[159],"freely":[162],"available":[163],"on":[164],"GitHub.":[165]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}