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kfuku52 / csubst

Molecular convergence detection
BSD 3-Clause "New" or "Revised" License
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How to identify convergent sites by csubst? #58

Open xinghua1001 opened 5 months ago

xinghua1001 commented 5 months ago

Hi,

Thank you for proposing the very smart new metric OmegaC and developing csubst. I'm not sure whether I understand it correctly, OmegaC is calculated by gene. After running csubst, we can know which gene is selected by filter the OmegaC. I'm particularly interested in the highly repetitive adaptive convergence. However, the question is that can we identify which amino acid site is the convergent sites underlying the phenotype by csubst, because I could not find this in the csubst results.

Thanks!

XL

kfuku52 commented 5 months ago

Thank you for using CSUBST. For the identification of convergent sites, please refer to this page: https://github.com/kfuku52/csubst/wiki/Mapping-convergent-substitutions-on-protein-structures

xinghua1001 commented 4 months ago

Hi Dr. Fukushima,

Is it possible that although OmegaC is significant, csubst site can not detect convergent sites. In my understanding, OmegaC is calculated at the gene level. Even if protein evolution rate is converged, the amino acids may not be the same among foreground lineages.

Thanks, Xinghua

kfuku52 commented 4 months ago

It is difficult to imagine a scenario where no convergent site is detected, if both omegaC_any2spe and OCN_any2spe are meaningfully high. I can assist you better if you could share your results.