PAUP: Multiple individuals as one branch
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5.4 years ago
cs4 • 0

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. 

paup phylogenetics trees • 1.2k views
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2
Entering edit mode
5.4 years ago
confusedious ▴ 420

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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