{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T16:33:59Z","timestamp":1732034039526},"reference-count":62,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2011,12,1]],"date-time":"2011-12-01T00:00:00Z","timestamp":1322697600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002269","type":"journal-article","created":{"date-parts":[[2011,12,3]],"date-time":"2011-12-03T04:40:23Z","timestamp":1322887223000},"page":"e1002269","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":19,"title":["Identifying Single Copy Orthologs in Metazoa"],"prefix":"10.1371","volume":"7","author":[{"given":"Christopher J.","family":"Creevey","sequence":"first","affiliation":[]},{"given":"Jean","family":"Muller","sequence":"additional","affiliation":[]},{"given":"Tobias","family":"Doerks","sequence":"additional","affiliation":[]},{"given":"Julie D.","family":"Thompson","sequence":"additional","affiliation":[]},{"given":"Detlev","family":"Arendt","sequence":"additional","affiliation":[]},{"given":"Peer","family":"Bork","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2011,12,1]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1126\/science.7542800","article-title":"Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.","volume":"269","author":"RD Fleischmann","year":"1995","journal-title":"Science"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/nar\/30.7.1575","article-title":"An efficient algorithm for large-scale detection of protein families.","volume":"30","author":"AJ Enright","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1126\/science.287.5461.2204","article-title":"Comparative genomics of the eukaryotes.","volume":"287","author":"GM Rubin","year":"2000","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1126\/science.278.5338.609","article-title":"Gene families: the taxonomy of protein paralogs and chimeras.","volume":"278","author":"S Henikoff","year":"1997","journal-title":"Science"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/nar\/29.1.22","article-title":"The COG database: new developments in phylogenetic classification of proteins from complete genomes.","volume":"29","author":"RL Tatusov","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1016\/S0959-437X(99)00029-5","article-title":"Orthologs, paralogs and genome comparisons.","volume":"9","author":"JP Gogarten","year":"1999","journal-title":"Curr Opin Genet Dev"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families.","volume":"278","author":"RL Tatusov","year":"1997","journal-title":"Science"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins.","volume":"19","author":"WM Fitch","year":"1970","journal-title":"Syst Zool"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/S0168-9525(02)02793-2","article-title":"Orthology, paralogy and proposed classification for paralog subtypes.","volume":"18","author":"EL Sonnhammer","year":"2002","journal-title":"Trends Genet"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"5849","DOI":"10.1073\/pnas.95.11.5849","article-title":"Measuring genome evolution.","volume":"95","author":"MA Huynen","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1006\/jmbi.2000.5197","article-title":"Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.","volume":"314","author":"M Remm","year":"2001","journal-title":"J Mol Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes.","volume":"13","author":"L Li","year":"2003","journal-title":"Genome Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"R31","DOI":"10.1186\/gb-2006-7-4-r31","article-title":"Benchmarking ortholog identification methods using functional genomics data.","volume":"7","author":"T Hulsen","year":"2006","journal-title":"Genome Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"D250","DOI":"10.1093\/nar\/gkm796","article-title":"eggNOG: automated construction and annotation of orthologous groups of genes.","volume":"36","author":"LJ Jensen","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"D271","DOI":"10.1093\/nar\/gkm845","article-title":"OrthoDB: the hierarchical catalog of eukaryotic orthologs.","volume":"36","author":"EV Kriventseva","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkn828","article-title":"Ensembl 2009.","volume":"37","author":"TJ Hubbard","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.1093\/bioinformatics\/btm295","article-title":"OMA Browser\u2013exploring orthologous relations across 352 complete genomes.","volume":"23","author":"A Schneider","year":"2007","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"3355","DOI":"10.1016\/j.febslet.2005.04.006","article-title":"Consistency of genome-based methods in measuring Metazoan evolution.","volume":"579","author":"EM Zdobnov","year":"2005","journal-title":"FEBS Lett"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.tig.2006.10.004","article-title":"Quantification of insect genome divergence.","volume":"23","author":"EM Zdobnov","year":"2007","journal-title":"Trends Genet"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e22099","DOI":"10.1371\/journal.pone.0022099","article-title":"Universally distributed single-copy genes indicate a constant rate of horizontal transfer.","volume":"6","author":"CJ Creevey","year":"2011","journal-title":"PLoS One"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/42711","article-title":"Molecular evidence for an ancient duplication of the entire yeast genome.","volume":"387","author":"KH Wolfe","year":"1997","journal-title":"Nature"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1016\/0168-9525(96)20010-1","article-title":"Non-orthologous gene displacement.","volume":"12","author":"EV Koonin","year":"1996","journal-title":"Trends Genet"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1126\/science.1123061","article-title":"Toward automatic reconstruction of a highly resolved tree of life.","volume":"311","author":"FD Ciccarelli","year":"2006","journal-title":"Science"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"2551","DOI":"10.1098\/rspb.2004.2864","article-title":"Does a tree-like phylogeny only exist at the tips in the prokaryotes?","volume":"271","author":"CJ Creevey","year":"2004","journal-title":"Proc Biol Sci"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1038\/nature02053","article-title":"Genome-scale approaches to resolving incongruence in molecular phylogenies.","volume":"425","author":"A Rokas","year":"2003","journal-title":"Nature"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/nature06614","article-title":"Broad phylogenomic sampling improves resolution of the animal tree of life.","volume":"452","author":"CW Dunn","year":"2008","journal-title":"Nature"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1093\/bioinformatics\/btm071","article-title":"CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.","volume":"23","author":"G Parra","year":"2007","journal-title":"Bioinformatics"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1186\/1471-2164-9-548","article-title":"A genome survey of Moniliophthora perniciosa gives new insights into Witches&apos; Broom Disease of cacao.","volume":"9","author":"JM Mondego","year":"2008","journal-title":"BMC Genomics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"R94","DOI":"10.1186\/gb-2009-10-9-r94","article-title":"De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data.","volume":"10","author":"S Diguistini","year":"2009","journal-title":"Genome Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1038\/nature06784","article-title":"The genome of the model beetle and pest Tribolium castaneum.","volume":"452","author":"S Richards","year":"2008","journal-title":"Nature"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e17034","DOI":"10.1371\/journal.pone.0017034","article-title":"Error and error mitigation in low-coverage genome assemblies.","volume":"6","author":"MJ Hubisz","year":"2011","journal-title":"PLoS One"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1471-2105-12-11","article-title":"OrthoInspector: comprehensive orthology analysis and visual exploration.","volume":"12","author":"B Linard","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1002\/bies.201100062","article-title":"Orthology prediction methods: A quality assessment using curated protein families.","volume":"33","author":"K Trachana","year":"2011","journal-title":"Bioessays"},{"key":"ref34","first-page":"57","article-title":"Reconciled trees and incongruent gene and species trees.","author":"RD Page","year":"1997"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1126\/science.1147112","article-title":"Genome-wide experimental determination of barriers to horizontal gene transfer.","volume":"318","author":"R Sorek","year":"2007","journal-title":"Science"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1006\/mpev.1996.0390","article-title":"From gene to organismal phylogeny: reconciled trees and the gene tree\/species tree problem.","volume":"7","author":"RD Page","year":"1997","journal-title":"Mol Phylogenet Evol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"R296","DOI":"10.1016\/j.cub.2005.04.001","article-title":"Animal phylogeny: fatal attraction.","volume":"15","author":"MJ Telford","year":"2005","journal-title":"Curr Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.","volume":"25","author":"SF Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1101\/gr.095026.109","article-title":"Recent de novo origin of human protein-coding genes.","volume":"19","author":"DG Knowles","year":"2009","journal-title":"Genome Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1126\/science.1080049","article-title":"The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.","volume":"298","author":"P Dehal","year":"2002","journal-title":"Science"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"4261","DOI":"10.1098\/rspb.2009.0896","article-title":"Assessing the root of bilaterian animals with scalable phylogenomic methods.","volume":"276","author":"A Hejnol","year":"2009","journal-title":"Proc Biol Sci"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"e1000703","DOI":"10.1371\/journal.pcbi.1000703","article-title":"Getting started in gene orthology and functional analysis.","volume":"6","author":"G Fang","journal-title":"PLoS Comput Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"R16","DOI":"10.1186\/gb-2010-11-2-r16","article-title":"2\u00d7 genomes\u2013depth does matter.","volume":"11","author":"MC Milinkovitch","journal-title":"Genome Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1186\/gb-2011-12-2-401","article-title":"Considerations for the inclusion of 2\u00d7 mammalian genomes in phylogenetic analyses.","volume":"12","author":"AJ Vilella","year":"2011","journal-title":"Genome Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput.","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1080\/10635150701472164","article-title":"Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.","volume":"56","author":"G Talavera","year":"2007","journal-title":"Syst Biol"},{"key":"ref47","first-page":"164","article-title":"Phylip - phylogeny inference package (version 3.2).","volume":"5","author":"J Felsenstein","year":"1989","journal-title":"Cladistics"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.","volume":"52","author":"S Guindon","year":"2003","journal-title":"Syst Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.","volume":"23","author":"I Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1101\/gr.3266405","article-title":"Complex genomic rearrangements lead to novel primate gene function.","volume":"15","author":"FD Ciccarelli","year":"2005","journal-title":"Genome Res"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/btp651","article-title":"AQUA: automated quality improvement for multiple sequence alignments.","volume":"26","author":"J Muller","year":"2010","journal-title":"Bioinformatics"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1093\/bioinformatics\/btg133","article-title":"RASCAL: rapid scanning and correction of multiple sequence alignments.","volume":"19","author":"JD Thompson","year":"2003","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1093\/bioinformatics\/bti020","article-title":"Clann: investigating phylogenetic information through supertree analyses.","volume":"21","author":"CJ Creevey","year":"2005","journal-title":"Bioinformatics"},{"key":"ref54","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bia01es00","article-title":"Sequence file format conversion with command-line readseq.","author":"D Gilbert","year":"2003","journal-title":"Curr Protoc Bioinformatics Appendix 1: Appendix 1E"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"R130","DOI":"10.1186\/gb-2009-10-11-r130","article-title":"BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.","volume":"10","author":"C Wu","year":"2009","journal-title":"Genome Biol"},{"key":"ref56","article-title":"R: A language and environment for statistical computing.","year":"2009"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"5736","DOI":"10.1091\/mbc.E05-06-0508","article-title":"Sequence and comparative genomic analysis of actin-related proteins.","volume":"16","author":"J Muller","year":"2005","journal-title":"Mol Biol Cell"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"W535","DOI":"10.1093\/nar\/gki423","article-title":"PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology.","volume":"33","author":"PE Saebo","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","article-title":"NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.","volume":"35","author":"KD Pruitt","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/S0959-440X(96)80056-X","article-title":"Hidden Markov models.","volume":"6","author":"SR Eddy","year":"1996","journal-title":"Curr Opin Struct Biol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1093\/oxfordjournals.molbev.a025808","article-title":"BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.","volume":"14","author":"O Gascuel","year":"1997","journal-title":"Mol Biol Evol"},{"key":"ref62","article-title":"PAUP*.","author":"DL Swofford","year":"2002"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002269","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T01:25:32Z","timestamp":1588987532000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002269"}},"subtitle":[],"editor":[{"given":"Adam","family":"Siepel","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2011,12,1]]},"references-count":62,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2011,12,1]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002269","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,12,1]]}}}