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Previously it was only possible to estimate phylogenetic trees with distance methods in R. phangorn, now offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses.<\/jats:p><jats:p>Availability: \u00a0phangorn can be obtained through the CRAN homepage http:\/\/cran.r-project.org\/web\/packages\/phangorn\/index.html. phangorn is licensed under GPL 2.<\/jats:p><jats:p>Contact: \u00a0klaus.kschliep@snv.jussieu.fr<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq706","type":"journal-article","created":{"date-parts":[[2010,12,18]],"date-time":"2010-12-18T03:20:38Z","timestamp":1292642438000},"page":"592-593","source":"Crossref","is-referenced-by-count":3643,"title":["phangorn: phylogenetic analysis in R"],"prefix":"10.1093","volume":"27","author":[{"given":"Klaus Peter","family":"Schliep","sequence":"first","affiliation":[{"name":"UMR CNRS 7138 Syst\u00e9matique, Adaptation, Evolution, Universit\u00e9 Pierre et Marie Curie, Mus\u00e9um National d'Histoire Naturelle, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,12,17]]},"reference":[{"key":"2023012511580764200_B1","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":"Guindon","year":"2003","journal-title":"Syst. 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