Question: PAUP: Multiple individuals as one branch
0
gravatar for cs4
3.9 years ago by
cs40
United States
cs40 wrote:

Hello,

I'm attempting to use PAUP* to make a tree. I have 80 individuals that make up 6 different species. When I make a tree now, I have 80 different branches and I would like to have 6 total branches instead of 80 branches. Is there any way to collapse all the individuals of one species into one branch to allow for a tree with only the 6 desired branches?

Thank you for any help you can offer. 

trees phylogenetics paup • 1.0k views
ADD COMMENTlink modified 3.9 years ago by confusedious420 • written 3.9 years ago by cs40
2
gravatar for confusedious
3.9 years ago by
confusedious420
Australia
confusedious420 wrote:

The easiest approach here would be to use a function like 'drop.tips' in the R package 'ape' to trim terminal branches until your terminal-most branch ends at the node from which all of your individuals within the one species radiate. You would need to repeat this process for each species.

I cannot think of an automated approach to doing this as most programs don't have a way of knowing what your definition of a species is.

Another option might be to use the software 'SplitsTree' to visualise your network and prune individuals until your six-branch tree is apparent.

ADD COMMENTlink written 3.9 years ago by confusedious420
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1707 users visited in the last hour