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pgfoster / p4-phylogenetics

A Python phyloinformatic toolkit, and an implementation of tree-heterogeneous models of evolution
GNU General Public License v2.0
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Request for understanding the nonstationary base composition simulation method in P4. #15

Closed BiodeB closed 2 years ago

BiodeB commented 2 years ago

Dear experts,

I'm a PhD scholar working on evolutionary biology, first time using this software P4 as I have noted some of renowned articles have done the simulations for base compositional heterogeneity across a given tree using P4. However, I'm unable to understand how to achieve it.

Therefore this is my humble request that it will be an immense help if you some kindly provide some python scripts used in P4 for the simulation of base composition heterogeneity among lineages.

Thanking you, Debajyoti

pgfoster commented 2 years ago

Hi Debajyoti. There are examples in the share/Examples folder that might help. For example, see share/Examples/H_calcLike/D_heteroOnTree/sSim.py or share/Examples/H_calcLike/H_remarkable/sSim.py. Good luck with it.