PAUP: Multiple individuals as one branch

Question

[cs4]

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.

Answer 1

[confusedious]

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.