{"id":"https://openalex.org/W4386356042","doi":"https://doi.org/10.1093/bioinformatics/btad540","title":"AliSim-HPC: parallel sequence simulator for phylogenetics","display_name":"AliSim-HPC: parallel sequence simulator for phylogenetics","publication_year":2023,"publication_date":"2023-09-01","ids":{"openalex":"https://openalex.org/W4386356042","doi":"https://doi.org/10.1093/bioinformatics/btad540","pmid":"https://pubmed.ncbi.nlm.nih.gov/37656933"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad540","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad540","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad540/51331800/btad540.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad540/51331800/btad540.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072480273","display_name":"Nhan Ly-Trong","orcid":"https://orcid.org/0000-0001-5668-5027"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Nhan Ly-Trong","raw_affiliation_strings":["School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia"],"affiliations":[{"raw_affiliation_string":"School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024994202","display_name":"Giuseppe M. J. Barca","orcid":"https://orcid.org/0000-0001-5109-4279"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Giuseppe M J Barca","raw_affiliation_strings":["School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia"],"affiliations":[{"raw_affiliation_string":"School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019880902","display_name":"B\u00f9i Quang Minh","orcid":"https://orcid.org/0000-0002-5535-6560"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Bui Quang Minh","raw_affiliation_strings":["School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia"],"affiliations":[{"raw_affiliation_string":"School of Computing, College of Engineering, Computing and Cybernetics, Australian National University , Canberra, ACT 2600, Australia","institution_ids":["https://openalex.org/I118347636"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5072480273"],"corresponding_institution_ids":["https://openalex.org/I118347636"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.48,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.89391237,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"39","issue":"9","first_page":null,"last_page":null},"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/T11269","display_name":"Algorithms and Data Compression","score":0.9674999713897705,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.9591000080108643,"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/computer-science","display_name":"Computer science","score":0.8120508193969727},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7144371867179871},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6907161474227905},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.6855347156524658},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6131361126899719},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5888715982437134},{"id":"https://openalex.org/keywords/message-passing-interface","display_name":"Message Passing Interface","score":0.5787967443466187},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5358288288116455},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.48295658826828003},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.45287901163101196},{"id":"https://openalex.org/keywords/computer-cluster","display_name":"Computer cluster","score":0.4495297372341156},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.4251119792461395},{"id":"https://openalex.org/keywords/message-passing","display_name":"Message passing","score":0.24504831433296204},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.21795609593391418},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21220606565475464},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15161076188087463},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0896146297454834}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8120508193969727},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7144371867179871},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6907161474227905},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.6855347156524658},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6131361126899719},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5888715982437134},{"id":"https://openalex.org/C166782233","wikidata":"https://www.wikidata.org/wiki/Q127879","display_name":"Message Passing Interface","level":3,"score":0.5787967443466187},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5358288288116455},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.48295658826828003},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.45287901163101196},{"id":"https://openalex.org/C29140674","wikidata":"https://www.wikidata.org/wiki/Q206637","display_name":"Computer cluster","level":2,"score":0.4495297372341156},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.4251119792461395},{"id":"https://openalex.org/C854659","wikidata":"https://www.wikidata.org/wiki/Q1859284","display_name":"Message passing","level":2,"score":0.24504831433296204},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.21795609593391418},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21220606565475464},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15161076188087463},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0896146297454834},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"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/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003205","descriptor_name":"Computing Methodologies","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad540","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad540","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad540/51331800/btad540.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37656933","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37656933","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10534053","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10534053","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10534053/pdf/btad540.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad540","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad540","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad540/51331800/btad540.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312169","display_name":"National Computational Infrastructure","ror":"https://ror.org/04yx6dh41"},{"id":"https://openalex.org/F4320315474","display_name":"Chan Zuckerberg Initiative","ror":"https://ror.org/02qenvm24"},{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320318839","display_name":"T\u1eadp \u0111o\u00e0n Vingroup - C\u00f4ng ty CP","ror":null},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386356042.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W50182133","https://openalex.org/W1593676244","https://openalex.org/W1867732144","https://openalex.org/W2008704758","https://openalex.org/W2012336267","https://openalex.org/W2016171324","https://openalex.org/W2026062398","https://openalex.org/W2086611351","https://openalex.org/W2088262090","https://openalex.org/W2111647009","https://openalex.org/W2117443107","https://openalex.org/W2125359798","https://openalex.org/W2127164334","https://openalex.org/W2130727968","https://openalex.org/W2135869163","https://openalex.org/W2148530335","https://openalex.org/W2157552136","https://openalex.org/W2162250327","https://openalex.org/W2286962642","https://openalex.org/W2716011421","https://openalex.org/W2949867654","https://openalex.org/W2950009653","https://openalex.org/W2973043487","https://openalex.org/W3005235420","https://openalex.org/W3037064900","https://openalex.org/W3041567587","https://openalex.org/W3111503053","https://openalex.org/W4225249066","https://openalex.org/W4229066198","https://openalex.org/W4233815609","https://openalex.org/W4247016878","https://openalex.org/W4295025031","https://openalex.org/W4299995088","https://openalex.org/W4386462191","https://openalex.org/W4401328094","https://openalex.org/W6639077426","https://openalex.org/W6678804063","https://openalex.org/W6681606956","https://openalex.org/W6696158138"],"related_works":["https://openalex.org/W3012895752","https://openalex.org/W4200215346","https://openalex.org/W2525033434","https://openalex.org/W4280533024","https://openalex.org/W4300992253","https://openalex.org/W2053585840","https://openalex.org/W1942762218","https://openalex.org/W1985270856","https://openalex.org/W1833720599","https://openalex.org/W3101274117"],"abstract_inverted_index":{"AliSim-HPC":[0],"is":[1],"open-source":[2],"and":[3],"available":[4],"as":[5],"part":[6],"of":[7],"the":[8],"new":[9],"IQ-TREE":[10],"version":[11],"v2.2.3":[12],"at":[13,19],"https://github.com/iqtree/iqtree2/releases":[14],"with":[15],"a":[16],"user":[17],"manual":[18],"http://www.iqtree.org/doc/AliSim.":[20]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}