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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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CodeML Site model err #26

Closed 32537 closed 11 months ago

32537 commented 1 year ago

The err is Warning: Hessian matrix may be unreliable for zero branch lengths and then is killed. I do not how to do it. Thanks for your help!

sabifo4 commented 11 months ago

Hi there,

This issue was addressed on the PAML Google Group in 2019 (see full discussion on the Google group). Ziheng gave the following answer:

this is a warning because some branch lengths are 0.  obviously if you have some identical sequences, some branch lengths will be 0.  i think you can ignore the warning.

Cheers!