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.
1 answer
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.
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