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abacus-gene / paml

PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, programs abort or do not run at all, etc.). Problems with input data and general questions should be posted at https://groups.google.com/g/pamlsoftware?pli
GNU General Public License v3.0
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Reg. free ration of #999 #23

Closed Prabhu89-code closed 1 year ago

Prabhu89-code commented 1 year ago

Dear Dr. Yang, I agree you have answered several times about this issue in google_groups. Can you kindly clarify by doubt on how to interpret this ratio whether branch with #999 is error or it can be a positive selection ?

Thanking you!

Regards, Dr. Prabhakaran S, Scientist, NIPGR.

ziheng-yang commented 1 year ago

999 for the dn/ds ratio is probably due to lack of synonymous differences. it's a bit like tossing a coin 5 or 10 times and observing no heads, so the probabilty of heads will be estimated to be 0. the likelihood ratio test is fine. but you should not interpret the dn/ds ratio literally. best, ziheng