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kfuku52 / csubst

Molecular convergence detection
BSD 3-Clause "New" or "Revised" License
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Species or gene tree? #59

Open bmm514 opened 5 months ago

bmm514 commented 5 months ago

Hi,

I am going to be using CSUBST in an exploratory manner on a number of genes from a phylogeny and I have both a species tree and gene trees (for each gene) available to me. Can you recommend the use of one over the other or will it not make too much difference?

Many thanks, Ben

kfuku52 commented 5 months ago

Thank you for considering the use of CSUBST. In this regard, please refer to this page: https://github.com/kfuku52/csubst/wiki/FAQ

bmm514 commented 5 months ago

Thank you for the quick response, I don't know how I missed this before! Just a quick clarification, CSUBST will still be able to detect convergent evolution for orthogroups with lineage-specific duplications in them? If so is there any limit to the number of lineage-specific duplications that can be present for a species?

kfuku52 commented 5 months ago

CSUBST does not have a hard limit on the number of duplications in the tree, but analyzing extremely large trees with thousands of genes may be challenging.