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#编者信息
熊荣川
明湖实验室
xiongrongchuan@126.com
http://blog.sciencenet.cn/u/Bearjazz
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。 |
https://cran.r-project.org/web/views/Phylogenetics.html |
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