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It implements popular methods employed in gene content analysis such as Dollo and Wagner parsimony, propensity for gene loss, as well as probabilistic methods involving a phylogenetic birth-and-death model.<\/jats:p><jats:p>Availability: Count is available as a stand-alone Java application, as well as an application bundle for MacOS X, at the web site http:\/\/www.iro.umontreal.ca\/\u223ccsuros\/gene_content\/count.html. It can also be launched using Java Webstart from the same site. The software is distributed under a BSD-style license. Source code is available upon request from the author.<\/jats:p><jats:p>Contact: \u00a0csuros@iro.umontreal.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq315","type":"journal-article","created":{"date-parts":[[2010,6,16]],"date-time":"2010-06-16T01:09:58Z","timestamp":1276650598000},"page":"1910-1912","source":"Crossref","is-referenced-by-count":423,"title":["Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood"],"prefix":"10.1093","volume":"26","author":[{"given":"Mikl\u00f3s","family":"Cs\u0171\u00f6s","sequence":"first","affiliation":[{"name":"Department of Computer Science and Operations Research, University of Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada"}]}],"member":"286","published-online":{"date-parts":[[2010,6,15]]},"reference":[{"key":"2023012508002343400_B1","doi-asserted-by":"crossref","first-page":"e9","DOI":"10.1093\/bioinformatics\/btl213","article-title":"Automatic clustering of orthologs and inparalogs shared by multiple genomes","volume":"22","author":"Alexeyenko","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012508002343400_B2","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1145\/974614.974657","article-title":"Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution","volume-title":"RECOMB '04: Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology.","author":"Arvestad","year":"2004"},{"key":"2023012508002343400_B3","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1145\/1502793.1502796","article-title":"The gene evolution model and computing its associated probabilities","volume":"56","author":"Arvestad","year":"2009","journal-title":"J. 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