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.

摘要：phangorn是一个用R语言进行系统发育重建和分析的软件包。以前只能用距离法分析系统发生树。Phangorn现在可以用距离法、最大简约法和最大似然法重建系统发育关系，执行Hadamard conjugation。扩展了通用ML框架，该包提供了估计混合模型和分区模型的可能性。此外，Phangron还提供了几种功能，用于比较系统发育树、系统发育模型或分支、模拟特征数据和进行一致性分析。