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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
I was wondering if there is a tree statistic that compares the topology of two trees which gives and indication of the degree of similarity or dissimilarity between the trees? | 我想知道是否有一个树的统计方法,比较两棵系统发育树的拓扑结构,给出和指示树之间的相似或不同程度? |
See these functions below, dist.topo is in library(Ape)
# check for similarity # do the two trees produced by MrBayes and raxML have the same topology?
all.equal(tree1, tree2, use.edge.length = FALSE)
# result = TRUE or FALSE.
# calculate the distance between the two tree, using default method. ( Penny and Hardy�s 1985)
dist.topo(tree1, tree2)
# result = numeric measure of distance | 请看R包Ape中的以下函数,dist.topo 查看相似性 分别由MrBayes 和raxML构建的两棵树,其拓扑结构一样吗?
使用默认参数,计算两棵树的距离
结果显示量化的距离 |
There is also SH.test (Shimodaira-Hasegawa test) in package phangorn
And the Icong index by de Vienne which only compares topology (See this website: http://www.ese.u-psud.fr/utilisateurs/devienne/index.html) | R语言包phangorn中有个SH.test (Shimodaira-Hasegawa test)函数,也可检验两棵系统发育树的相似性。 de Vienne提出的Icong指数只比较拓扑结构,到以下网址进一步了解详情。 |
To complete this discussion, the package distory computes Billera et al.'s geodesic distance between two trees. | 为了终结本讨论,R包distory可以计算由Billera等提出的两棵树之间测地距离。 |
参考文献: 【1】https://grokbase.com/t/r/r-sig-phylo/1133cx4fck/comparing-the-topology-of-two-trees 【2】注解:geodesic distance ,这个单词的中文翻译是测地距离,其实测地距离的意思就是在三维空间中,两点之间的最短路径,归根究底就是最短路径,在三维中间从一个点到另外一个点的路径有无数种,但是最短路径只有一条,那么这个最短路径的长度就是测地距离 geodesic distance。 --------------------- 作者:HNU_wang_chao 来源:CSDN 原文:https://blog.csdn.net/hnu_wang_chao/article/details/78612479 |
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