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phyloacc / PhyloAcc

PhyloAcc a software to detect the changes of conservation of a genomic region
GNU General Public License v3.0
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How to select convergent CNEs #28

Closed zzzchang closed 1 year ago

zzzchang commented 2 years ago

Dear author,

I have used PhyloAcc to calculate CNEs, I would like to ask how to filter the values of logBF1 and logBF2 based on the results obtained? If I want to filter the convergent evolution of multiple species, what should I do? Another question,how to count how many target species have evolved in each CNE?

Best regards Chang Zhang

xyz111131 commented 2 years ago

Is it resolved?

zzzchang commented 2 years ago

Dear author,

Thanks for quick replay. I still have a question about how to select convergent CNEs, If I set the target species’ posterior probability cutoff of >= 0.90 to define acceleration, Are there any requirements for the posterior probabilities of the control species? And are there any other parameters that need to be set?

Best regards Chang Zhang

xyz111131 commented 2 years ago

Dear Chang,

Thanks for the question. You might also set the cutoff for control species e.g. <= 0.1. Also, you could select the elements based on logBFs. If you want, you might adjust the CONSTOMIS parameter which controls to how likely missing species to be treated as accelerated.

Best, zhirui