phangorn：R 中的系统发育分析。
phangorn: phylogenetic analysis in R.
机构信息
UMR CNRS 7138 Systématique, Adaptation, Evolution, Université Pierre et Marie Curie, Muséum National d'Histoire Naturelle, Paris, France.
出版信息
Bioinformatics. 2011 Feb 15;27(4):592-3. doi: 10.1093/bioinformatics/btq706. Epub 2010 Dec 17.
SUMMARY
phangorn is a package for phylogenetic reconstruction and analysis in the R language. 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.
AVAILABILITY
phangorn can be obtained through the CRAN homepage http://cran.r-project.org/web/packages/phangorn/index.html. phangorn is licensed under GPL 2.
摘要
phangorn 是 R 语言中用于系统发育重建和分析的一个软件包。以前，在 R 中只能使用距离法估计系统发育树。现在，phangorn 提供了基于距离的方法、最大简约法或最大似然法（ML）和进行 Hadamard 共轭来重建系统发育的可能性。该软件包扩展了一般的 ML 框架，提供了估计混合和分区模型的可能性。此外，phangorn 还提供了用于比较树、系统发育模型或分裂、模拟特征数据和进行一致性分析的几个功能。
可用性
可以通过 CRAN 主页 http://cran.r-project.org/web/packages/phangorn/index.html 获得 phangorn。phangorn 根据 GPL 2 获得许可。
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