Comparing two phylogenies
3
3
Entering edit mode
5.6 years ago
Jautis ▴ 300

Hi, 

I have two phylogenies (1 genetic, 1 phenotypic) that I would like to compare. I know that they are different phylogenies (that much I can tell by looking/with all.equal from ape) and can generate an overall similarity from the var-covar or distance matrix (using a mantel test).

What I would like to do now is separately determine how similar the topology and branch length are. Does anybody know of a way to do this? 

Thanks!

 

phylogeny tree covariance • 4.3k views
ADD COMMENT
2
Entering edit mode
5.6 years ago
Shicheng Guo ★ 8.6k

1, quantitative: Shared branches / total branches

2, visual: circular graph 

 

ADD COMMENT
2
Entering edit mode
5.6 years ago
jhc ★ 2.9k

you may want to take a look at ete-compare. It allows one to compute unweighted robinson-foulds distances, as well as the number of partitions/branches in one tree that are not found in the other. It permits also to dump the matches and mismatches between trees.   

ADD COMMENT
1
Entering edit mode
5.6 years ago
Brice Sarver ★ 3.6k

There are a variety of metrics that compute distances between two trees. The most commonly used is the Robinson-Foulds (RF) distance, which looks for nodes present in one tree and vice versa. There are also methods that take branch lengths into account directly, like the Kuhner-Felsenstein Distance. These methods are implemented in R in several packages. Be aware that you will want your trees to have branch lengths in the same units if you are going to use any method that takes them into account.

ADD COMMENT

Login before adding your answer.

Traffic: 1542 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6