沉闷科学的掘墓人分享 http://blog.sciencenet.cn/u/Bearjazz

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每日翻译20190427

已有 1797 次阅读 2019-4-27 07:03 |个人分类:翻译作品|系统分类:科研笔记| R语言, 系统发育, 祖先特征重建, 溯祖理论

#编者信息

熊荣川

明湖实验室

xiongrongchuan@126.com

http://blog.sciencenet.cn/u/Bearjazz

 

Ancestral   state reconstruction : Continuous characters can be   reconstructed using maximum likelihood, generalised least squares or independent contrasts   in ape.   Root ancestral character states under Brownian motion or Ornstein-Uhlenbeck   models can be reconstructed in ouch,   though ancestral states at the internal nodes are not. Discrete characters   can be reconstructed using a variety of Markovian models that parameterize   the transition rates among states using apemarkophylo can   fit a broad set of discrete character types with models that can incorporate constrained substitution   rates, rate partitioning across sites, branch-specific rates, sampling bias,   and non-stationary root probabilities. phytools can   do stochastic character mapping of traits on trees.

 

祖先状态重建:连续性特征可以使用apee包中最大似然法、一般最小二乘法或独立对比方法重建。在ouch中可用Brownian   motionOrnstein-Uhlenbeck模型,确定根部祖先特征状态,而内部节点的祖先状态则不能。使用ape状态之间的转换率参数化后,离散特征可以使用各种马尔可夫模型重建。markophylo可以适配广泛的离散特征类型,设定约束替换率、跨位点的速率分配、特定分支速率、采样偏差和非静态根概率的模型。phytools可以在树上进行随机特征标注。

https://cran.r-project.org/web/views/Phylogenetics.html

 

 




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