GitHub - mtholder/gene-tree-divers-sim: scripts for testing the effect of using a gene tree instead of a species tree to estimate changes in speciation rates

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scripts for testing the effect of using a gene tree instead of a species tree to estimate changes in speciation rates

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
2mccoal.py		2mccoal.py
README.txt		README.txt
bdtree.py		bdtree.py
invoc.sh		invoc.sh
master.py		master.py

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MCcoal must be on your PATH.

Download http://abacus.gene.ucl.ac.uk/software/MCMCcoal.html
unpack it and build it.
Put the MCcoal subdirectory on your PATH. In bash this is something like:
     export PATH=$HOME/builds/phylo/MCMCcoal/MCcoal:$PATH
     
invoc.sh is simply a call to master.py

Use:
    master.py -h
to see all of the help options.