{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:51Z","timestamp":1772138091620,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2018,10,15]],"date-time":"2018-10-15T00:00:00Z","timestamp":1539561600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007316","name":"Klaus Tschira Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007316","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","award":["STA 860\/4-2"],"award-info":[{"award-number":["STA 860\/4-2"]}],"id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Coalescent- and reconciliation-based methods are now widely used to infer species phylogenies from genomic data. They typically use per-gene phylogenies as input, which requires conducting multiple individual tree inferences on a large set of multiple sequence alignments (MSAs). At present, no easy-to-use parallel tool for this task exists. Ad hoc scripts for this purpose do not only induce additional implementation overhead, but can also lead to poor resource utilization and long times-to-solution. We present ParGenes, a tool for simultaneously determining the best-fit model and inferring maximum likelihood (ML) phylogenies on thousands of independent MSAs using supercomputers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>ParGenes executes common phylogenetic pipeline steps such as model-testing, ML inference(s), bootstrapping and computation of branch support values via a single parallel program invocation. We evaluated ParGenes by inferring &amp;gt; 20\u00a0000 phylogenetic gene trees with bootstrap support values from Ensembl Compara and VectorBase alignments in 28\u2009h on a cluster with 1024 nodes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>GNU GPL at https:\/\/github.com\/BenoitMorel\/ParGenes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary material is available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty839","type":"journal-article","created":{"date-parts":[[2018,10,12]],"date-time":"2018-10-12T15:16:07Z","timestamp":1539357367000},"page":"1771-1773","source":"Crossref","is-referenced-by-count":72,"title":["ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6286-4419","authenticated-orcid":false,"given":"Benoit","family":"Morel","sequence":"first","affiliation":[{"name":"Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, Germany"}]},{"given":"Alexey M","family":"Kozlov","sequence":"additional","affiliation":[{"name":"Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, Germany"}]},{"given":"Alexandros","family":"Stamatakis","sequence":"additional","affiliation":[{"name":"Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg, Germany"},{"name":"Department of Informatics, Karlsruhe Institute of Technology, Institute of Theoretical Informatics, Postfach 6980, Karlsruhe, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,10,15]]},"reference":[{"key":"2023013107484458900_bty839-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bioinformatics\/btg1000","article-title":"Bayesian gene\/species tree reconciliation and orthology analysis using MCMC","volume":"19","author":"Arvestad","year":"2003","journal-title":"Bioinformatics"},{"key":"2023013107484458900_bty839-B2","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1101\/gr.141978.112","article-title":"Genome-scale coestimation of species and gene trees","volume":"23","author":"Boussau","year":"2012","journal-title":"Genome Res"},{"key":"2023013107484458900_bty839-B3","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1093\/nar\/gku1117","article-title":"VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases","volume":"43","author":"Emrich","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023013107484458900_bty839-B4","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1093\/bioinformatics\/btv184","article-title":"Examl version 3: a tool for phylogenomic analyses on supercomputers","volume":"31","author":"Kozlov","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013107484458900_bty839-B5","author":"Kozlov","year":"2018"},{"key":"2023013107484458900_bty839-B6","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/molbev\/msm052","article-title":"A likelihood framework to measure horizontal gene transfer","volume":"24","author":"Linz","year":"2007","journal-title":"Mol. 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