annotating Multiple Phylogenetic trees on the basis of color

Question

[Sourabh J]

Hello everyone,

I have multiple phylogenetic trees (more than 5000) in newick format and I want to color them according to their tip label. I know this can be done in package ape and phytools in R, but, I am not getting how to annotate multiple trees at once using these packages. What I want is graphical output with 1. colored annotation, 2. Midpoint root, 3. laddrise descending

Can someone please help me how to made this possible ?

Answer 1

[moranr]

Have you had a look at ETE form Python ? Its super easy to use if you know python.

http://etetoolkit.org/docs/latest/index.html

1)Traverse each node of a tree, or each terminal branch 2) Add a color attribute to each.
3) Then render the image.

Goodluck, R

Answer 2

[DG]

If the R packages you are interested in don't offer a method for doing multiple trees simultaneously as a convenience method, which isn't that surprising, you can always write an R script to iterate over the trees and do them sequentially. Same goes for ETE in Python as @moranr suggested. You can take advantage of parallele processing fairly easily in Python with Map/Reduce or similar with the Multiprocessing package.