Codeml (v 4v4d) using fixed kappa value, reports wrong kappa - Githubissues

cjfields commented 9 years ago

Author Name: Janet Young (Janet Young) Original Redmine Issue: 3331, https://redmine.open-bio.org/issues/3331 Original Date: 2012-03-06 Original Assignee: Bioperl Guts

Hi there,

After a long absence, I’ve started using Bioperl to run PAML again. Apologies if I’m bringing up another one of those annoying “PAML changed and broke the parser” kinds of issues… Is PAML v4.4d supported?

I found a minor bug/issue I thought you might want to know about: if I set up a ka_ks_factory and specify fix_kappa = 1, then I recover the kappa via get_MLmatrix, it actually reports to me the omega (not the kappa). I’ll attach a script that shows this (I’ll include output as comments in the script). I think the example script should explain everything, but please let me know if you need more details…

thanks very much,

Janet Young

Dr. Janet Young

Tapscott and Malik labs

Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA.

email: jayoung …at… fhcrc.org

cjfields commented 9 years ago

Original Redmine Comment Author Name: Jason Stajich Original Date: 2012-03-13T16:53:53Z

You are definitely the first to use/report on 4.4d… hopefully someone can look at it quickly as it sounds like a quick fix.

cjfields commented 9 years ago

Original Redmine Comment Author Name: Daisie Huang Original Date: 2012-06-20T23:02:49Z

Fixed at https://github.com/daisieh/bioperl-live/zipball/bug3331

carandraug commented 7 years ago

Fixed and merged into bioperl-live with bioperl/bioperl-live@f7b9e38b1060738f9b

bioperl / bioperl-run

Codeml (v 4v4d) using fixed kappa value, reports wrong kappa #35