Importing nexus-formatted tree (e.g. BEAST tree) into R as a phylo object with node labels
0
0
Entering edit mode
17 months ago
al-ash ▴ 200

I'm trying to import a nexus tree (from BEAST) as a phylo object with node information (I'm specifically interested in the "posterior" values). The methods I tried fail: 1) importing with ape::read.nexus() does not import node labels 2) importing with treeio::read.beast() and then converting to phylo with "ape::as.phylo()" drops the node labels. 3) converting beast tree in nexus format to newick format in FigTree (do the newick can be imported e.g. with ape::read.tree as a phylo object with node labels) also drops node labels.

I'm specifically interested in "BEAST tree file -> phylo object in R with node labels" import because my other code is using phylo objects to manipulate trees (imported with node labels from newick format).

Thanks for any hints and suggestions! Ales

BEAST nexus phylo treedata R • 496 views
ADD COMMENT
0
Entering edit mode

I have the same concern. Any solution to this?

ADD REPLY

Login before adding your answer.

Traffic: 3085 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