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cwhidden / sprspace

A collection of shell and perl scripts for quantifying MCMC exploration of subtree prune-and-regraft tree space in MrBayes posteriors.
GNU General Public License v3.0
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Why no support for BEAST tree output? #1

Open andersgs opened 8 years ago

andersgs commented 8 years ago

Very interesting paper, and code. But, wish you supported BEAST output too.

Anders.

jjmccollum commented 4 months ago

I realize I'm nearly ten years late on this, but I was also interested in generating an SPR graph of a posterior distribution of trees sampled in BEAST 2. I did some playing around and found that it's not much trouble to convert BEAST 2 .trees and .log files to MrBayes .t and .p files with a Python script. In case anyone reading this is in the same situation, you may be interested in the beast2bayes.py script at https://github.com/jjmccollum/beast2bayes.

That said, it may be just as easy to modify split_nexus_tree.pl to do the additional step of stripping bracketed attributes (e.g., [&rate...]) and root branch lengths from the trees in BEAST outputs and to modify process_mrbayes_posterior.bash into a process_beast_posterior.bash script on this end.