{"id":"https://openalex.org/W4387346565","doi":"https://doi.org/10.1145/3584371.3612996","title":"Phylogenomics using Compression Distances: Incorporating Rate Heterogeneity and Amino Acid Properties","display_name":"Phylogenomics using Compression Distances: Incorporating Rate Heterogeneity and Amino Acid Properties","publication_year":2023,"publication_date":"2023-09-03","ids":{"openalex":"https://openalex.org/W4387346565","doi":"https://doi.org/10.1145/3584371.3612996"},"language":"en","primary_location":{"id":"doi:10.1145/3584371.3612996","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612996","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612996","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612996","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087747590","display_name":"Edward L. Braun","orcid":"https://orcid.org/0000-0003-1643-5212"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Edward L Braun","raw_affiliation_strings":["Biology, University of Florida, Gainesville, FL, USA"],"raw_orcid":"https://orcid.org/0000-0003-1643-5212","affiliations":[{"raw_affiliation_string":"Biology, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5087747590"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":0.2999,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.64019581,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9944000244140625,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9939000010490417,"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/phylogenomics","display_name":"Phylogenomics","score":0.9019674062728882},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.618169903755188},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5995410084724426},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5698778629302979},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5592900514602661},{"id":"https://openalex.org/keywords/sorting","display_name":"Sorting","score":0.5098645091056824},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5045207738876343},{"id":"https://openalex.org/keywords/attraction","display_name":"Attraction","score":0.4806000888347626},{"id":"https://openalex.org/keywords/compression","display_name":"Compression (physics)","score":0.47926780581474304},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4735915958881378},{"id":"https://openalex.org/keywords/data-compression","display_name":"Data compression","score":0.4542645812034607},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.35717156529426575},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3235585391521454},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.29932576417922974},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25969088077545166},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2540019750595093},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21806678175926208},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.12707430124282837},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11058938503265381},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.09481412172317505},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07967504858970642}],"concepts":[{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.9019674062728882},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.618169903755188},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5995410084724426},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5698778629302979},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5592900514602661},{"id":"https://openalex.org/C111696304","wikidata":"https://www.wikidata.org/wiki/Q2303697","display_name":"Sorting","level":2,"score":0.5098645091056824},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5045207738876343},{"id":"https://openalex.org/C2778364177","wikidata":"https://www.wikidata.org/wiki/Q2247133","display_name":"Attraction","level":2,"score":0.4806000888347626},{"id":"https://openalex.org/C180016635","wikidata":"https://www.wikidata.org/wiki/Q2712821","display_name":"Compression (physics)","level":2,"score":0.47926780581474304},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4735915958881378},{"id":"https://openalex.org/C78548338","wikidata":"https://www.wikidata.org/wiki/Q2493","display_name":"Data compression","level":2,"score":0.4542645812034607},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35717156529426575},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3235585391521454},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.29932576417922974},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25969088077545166},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2540019750595093},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21806678175926208},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.12707430124282837},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11058938503265381},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.09481412172317505},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07967504858970642},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3584371.3612996","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612996","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612996","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3584371.3612996","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3584371.3612996","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3584371.3612996","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G2722506542","display_name":null,"funder_award_id":"1655683","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3874960311","display_name":null,"funder_award_id":"DEB-1655683","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":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387346565.pdf"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1517039185","https://openalex.org/W1638203394","https://openalex.org/W1887892324","https://openalex.org/W1966972227","https://openalex.org/W1977358834","https://openalex.org/W2015800458","https://openalex.org/W2037654474","https://openalex.org/W2041101954","https://openalex.org/W2043066342","https://openalex.org/W2052432722","https://openalex.org/W2109846272","https://openalex.org/W2118029157","https://openalex.org/W2119837484","https://openalex.org/W2125598538","https://openalex.org/W2127713506","https://openalex.org/W2128859735","https://openalex.org/W2139736670","https://openalex.org/W2140099453","https://openalex.org/W2144221002","https://openalex.org/W2165999027","https://openalex.org/W2255592388","https://openalex.org/W2266439690","https://openalex.org/W2600349519","https://openalex.org/W2601425645","https://openalex.org/W2614081736","https://openalex.org/W2771760123","https://openalex.org/W2807954510","https://openalex.org/W2911827168","https://openalex.org/W2951464304","https://openalex.org/W2953500616","https://openalex.org/W2963815633","https://openalex.org/W2963984870","https://openalex.org/W3005235420","https://openalex.org/W3020693699","https://openalex.org/W3099172549","https://openalex.org/W3102172121","https://openalex.org/W3108747777","https://openalex.org/W3131548182","https://openalex.org/W3192606035","https://openalex.org/W4226213413","https://openalex.org/W4307255791","https://openalex.org/W4319963696","https://openalex.org/W4322493002","https://openalex.org/W4367173724"],"related_works":["https://openalex.org/W3029188025","https://openalex.org/W2004941704","https://openalex.org/W3006141270","https://openalex.org/W2169952341","https://openalex.org/W2116404931","https://openalex.org/W33088422","https://openalex.org/W2163632697","https://openalex.org/W1977936579","https://openalex.org/W1806394644","https://openalex.org/W2905265174"],"abstract_inverted_index":{"Efforts":[0],"to":[1,78,94,97,112,116,159],"reconstruct":[2],"the":[3,12,18,34,37,104,169,171],"tree":[4,44,161],"of":[5,39,47,73,82],"life":[6],"have":[7],"a":[8,30,79,164],"long":[9,58,98,117],"history,":[10],"but":[11],"field":[13,35],"has":[14],"changed":[15],"fundamentally":[16],"in":[17,33,152,176],"genomic":[19],"era.":[20],"Phylogenomics":[21],"examines":[22],"evolutionary":[23],"relationships":[24],"using":[25,163],"very":[26],"large":[27],"datasets,":[28],"so":[29],"major":[31,80],"problem":[32],"is":[36],"development":[38],"unbiased":[40],"computational":[41],"methods":[42],"for":[43,126],"inference.":[45],"Sources":[46],"bias":[48],"include":[49],"sequence":[50,68],"alignment":[51,69],"errors,":[52],"discordance":[53,83],"among":[54,84],"gene":[55,85],"trees,":[56],"and":[57,71,120],"branch":[59,99,118],"attraction.":[60,100],"Distances":[61],"based":[62,138],"on":[63,139],"data":[64],"compression":[65,91,107,124,149],"can":[66,109],"address":[67],"errors":[70],"analyses":[72],"distances":[74,92,108,125,133,150],"may":[75],"be":[76,95,110,113],"robust":[77],"source":[81],"trees":[86],"(incomplete":[87],"lineage":[88],"sorting).":[89],"However,":[90],"appear":[93],"susceptible":[96],"This":[101],"study":[102,154],"tested":[103],"hypothesis":[105],"that":[106,122,166],"modified":[111,148],"more":[114,144],"resistant":[115],"attraction":[119],"found":[121],"correcting":[123],"multiple":[127],"substitutions":[128],"improved":[129],"their":[130,140],"behavior.":[131],"Calculating":[132],"after":[134],"grouping":[135],"amino":[136],"acids":[137],"physicochemical":[141],"properties":[142],"incorporated":[143],"biological":[145],"information.":[146],"The":[147],"used":[151],"this":[153],"also":[155],"made":[156],"it":[157],"possible":[158],"estimate":[160],"support":[162,174],"method":[165],"closely":[167],"resembles":[168],"bootstrap,":[170],"most":[172],"popular":[173],"metric":[175],"phylogenomics.":[177]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2025-12-22T23:10:17.713674","created_date":"2025-10-10T00:00:00"}
