{"id":"https://openalex.org/W2570474257","doi":"https://doi.org/10.1093/bioinformatics/btw779","title":"pHMM-tree: phylogeny of profile hidden Markov models","display_name":"pHMM-tree: phylogeny of profile hidden Markov models","publication_year":2016,"publication_date":"2016-12-02","ids":{"openalex":"https://openalex.org/W2570474257","doi":"https://doi.org/10.1093/bioinformatics/btw779","mag":"2570474257","pmid":"https://pubmed.ncbi.nlm.nih.gov/28062446"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw779","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw779","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/1093/25149935/btw779.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/1093/25149935/btw779.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002793806","display_name":"Luyang Huo","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Luyang Huo","raw_affiliation_strings":["College of Computer and Control Engineering, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100399265","display_name":"Han Zhang","orcid":"https://orcid.org/0000-0001-8498-3451"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Han Zhang","raw_affiliation_strings":["College of Computer and Control Engineering, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066566727","display_name":"Xueting Huo","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueting Huo","raw_affiliation_strings":["College of Computer and Control Engineering, Nankai University, Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054223009","display_name":"Yasong Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I102502594","display_name":"Northern Illinois University","ror":"https://ror.org/012wxa772","country_code":"US","type":"education","lineage":["https://openalex.org/I102502594"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yasong Yang","raw_affiliation_strings":["Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA","institution_ids":["https://openalex.org/I102502594"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028578817","display_name":"Xueqiong Li","orcid":"https://orcid.org/0000-0002-2364-4947"},"institutions":[{"id":"https://openalex.org/I102502594","display_name":"Northern Illinois University","ror":"https://ror.org/012wxa772","country_code":"US","type":"education","lineage":["https://openalex.org/I102502594"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xueqiong Li","raw_affiliation_strings":["Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA","institution_ids":["https://openalex.org/I102502594"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090843422","display_name":"Yanbin Yin","orcid":"https://orcid.org/0000-0001-7667-881X"},"institutions":[{"id":"https://openalex.org/I102502594","display_name":"Northern Illinois University","ror":"https://ror.org/012wxa772","country_code":"US","type":"education","lineage":["https://openalex.org/I102502594"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yanbin Yin","raw_affiliation_strings":["Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA","institution_ids":["https://openalex.org/I102502594"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5090843422","https://openalex.org/A5100399265"],"corresponding_institution_ids":["https://openalex.org/I102502594","https://openalex.org/I205237279"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3929,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.82806579,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"33","issue":"7","first_page":"1093","last_page":"1095"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5486999750137329,"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":0.5486999750137329,"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":0.06780000030994415,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.047600001096725464,"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/hidden-markov-model","display_name":"Hidden Markov model","score":0.6287375688552856},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5991111397743225},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5895059108734131},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5318930149078369},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5004091262817383},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4282693564891815},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41812044382095337},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.37552955746650696},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3437806963920593},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34104007482528687},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17633673548698425},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17251956462860107},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.13885939121246338},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09282630681991577},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09239760041236877}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.6287375688552856},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5991111397743225},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5895059108734131},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5318930149078369},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5004091262817383},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4282693564891815},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41812044382095337},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37552955746650696},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3437806963920593},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34104007482528687},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17633673548698425},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17251956462860107},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.13885939121246338},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09282630681991577},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09239760041236877}],"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw779","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw779","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/1093/25149935/btw779.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28062446","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28062446","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:5860389","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860389","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw779","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw779","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/7/1093/25149935/btw779.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1321143768","display_name":null,"funder_award_id":"(15JCYBJC18900)","funder_id":"https://openalex.org/F4320323993","funder_display_name":"Natural Science Foundation of Tianjin City"},{"id":"https://openalex.org/G6080771090","display_name":null,"funder_award_id":"R15 GM114706","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6109946439","display_name":null,"funder_award_id":"(1R15GM114706)","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6342795055","display_name":null,"funder_award_id":"15JCYBJC18900","funder_id":"https://openalex.org/F4320323993","funder_display_name":"Natural Science Foundation of Tianjin City"},{"id":"https://openalex.org/G7491376909","display_name":null,"funder_award_id":"1R15GM114706","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320323993","display_name":"Natural Science Foundation of Tianjin City","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2570474257.pdf","grobid_xml":"https://content.openalex.org/works/W2570474257.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2027542060","https://openalex.org/W2051210555","https://openalex.org/W2096234478","https://openalex.org/W2098425296","https://openalex.org/W2106868489","https://openalex.org/W2117077088","https://openalex.org/W2117486996","https://openalex.org/W2136280642","https://openalex.org/W2151831732","https://openalex.org/W4235848672"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082","https://openalex.org/W2362218761","https://openalex.org/W1974895455"],"abstract_inverted_index":{"Protein":[0],"families":[1,16,35,96],"are":[2,155],"often":[3],"represented":[4],"by":[5,20],"profile":[6],"hidden":[7],"Markov":[8],"models":[9],"(pHMMs).":[10],"Homology":[11],"between":[12],"two":[13],"distant":[14,129],"protein":[15,34,66,80,95,130],"can":[17],"be":[18,89],"determined":[19],"comparing":[21],"the":[22,27,37,121,125],"pHMMs.":[23,42],"Here":[24],"we":[25],"explored":[26],"idea":[28],"of":[29,33,40,57,71,93,124],"building":[30],"a":[31,45,83,90],"phylogeny":[32,92],"using":[36],"distance":[38],"matrix":[39],"their":[41,98],"We":[43,100],"developed":[44],"new":[46],"software":[47,136],"and":[48,73,77,113,133,142],"web":[49],"server":[50],"(pHMM-tree)":[51],"to":[52,104],"allow":[53],"four":[54],"major":[55],"types":[56],"inputs:":[58],"(i)":[59],"multiple":[60,64],"pHMM":[61,72,91],"files,":[62,68],"(ii)":[63],"aligned":[65,74],"sequence":[67,75],"(iii)":[69],"mixture":[70],"files":[76],"(iv)":[78],"unaligned":[79],"sequences":[81],"in":[82,120,139],"single":[84],"file.":[85],"The":[86],"output":[87],"will":[88],"different":[94],"delineating":[97],"relationships.":[99],"have":[101],"applied":[102],"pHMM-tree":[103],"build":[105],"phylogenies":[106],"for":[107],"CAZyme":[108],"(carbohydrate":[109],"active":[110],"enzyme)":[111],"classes":[112],"Pfam":[114],"clans,":[115],"which":[116],"attested":[117],"its":[118],"usefulness":[119],"phylogenetic":[122],"representation":[123],"evolutionary":[126],"relationship":[127],"among":[128],"families.":[131],"Availability":[132],"Implementation:":[134],"This":[135],"is":[137,143],"implemented":[138],"C/C":[140],"++":[141],"available":[144,156],"at":[145,157],"http://cys.bios.niu.edu/pHMM-Tree/source/.":[146],"Contact:":[147],"zhanghan@nankai.edu.cn":[148],"or":[149],"yyin@niu.edu.":[150],"Supplementary":[151,153],"information:":[152],"data":[154],"Bioinformatics":[158],"online.":[159]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}