Question

How to annotate nodes in trees using R?

1

Entering edit mode

6.8 years ago

Speed.Lee ▴ 30

Hi, I am a newbie in biology. Currently, I am working with R to generate trees (but not in biology, for other subjects). I just have some concern using phangron and ape (other packages of R is OK if they can solve this problem).

My data is like this, binary datasets.

Format of data

And what I want to generate are trees like this: all the characteristics made the difference are labelled in the tree (automatically, not point by me after generated the tree). I do not mind if they are annotated at nodes or on edges.

Tree format wanted

Is it possible? How can I do it? Thanks in advance for the comments.

R • 2.1k views

ADD COMMENT • link updated 6.8 years ago by Bioinformatics_NewComer ▴ 330 • written 6.8 years ago by Speed.Lee ▴ 30

score 0 · Answer 1 · 2017-06-15

0

Entering edit mode

6.8 years ago

Bioinformatics_NewComer ▴ 330

Check itol's website. Also, see http://docs.phylotoast.org/en/latest/scripts/iTol.html

ADD COMMENT • link 6.8 years ago by Bioinformatics_NewComer ▴ 330

1

Entering edit mode

Thanks, this is a great website, but I am afraid it is not so suitable for me because I need to finish it by R.

I found Last common ancestor method mentioned on the website might be helpful for this topic, so I decide to do some research on it. Thanks again for the help!