Phylogenetic   Inference: UPGMA, neighbour joining, bio-nj and   fast ME methods of phylogenetic reconstruction are all implemented in the   package ape. phangorn can   estimate trees using distance, parsimony, and likelihood. phyclust can   cluster sequences. phytools can   build trees using MRP supertree estimation and least squares. phylotools can   build supermatrices for analyses in other software. pastis can   use taxonomic information to make constraints for Bayesian tree   searches. outbreaker can   infer transmission trees for diseases, as well as other parameters of disease   spread. For more information on importing sequence data, see the Genetics task   view; pegas may   also be of use.

系统发育推断：UPGMA、邻接、Bio NJ和快速ME等系统发育重建方法均可在ape中实现。phangorn可以用距离法、简约法和似然法来估计系统发育树。phyclust可以对序列聚类。phytools可以利用MRP超树估计和最小二乘法构建系统发育树。phylotools可以构建超级矩阵，从而便于在其他软件中进一步分析。pastis可以使用分类信息对贝叶斯树搜索进行约束。outbreaker可以推断疾病的传播树，以及疾病传播的其他参数。有关导入序列数据的更多信息，请参见Genetics任务视图；也可以使用pegas。