[Bioperl-l] question about a PAML module

Rui Faria rui.faria at upf.edu
Sun Jan 31 12:17:09 EST 2010

Hi Dave,

we reported the bug on codeml about errors when the user gives its own tree file, some time ago. Did you have any chances to look at it?

We basically wanted to know your opinion on where the problem may be, since we are not the most experienced "perlers" on the planet :) 

I'm asking this because we have to deal with that right now. If someone could check where is the problem, to understand if it has an easy solution, that would be of great help.



-----Mensaje Original-----
De Dave Messina <David.Messina at sbc.su.se>
Enviado Jue 31/12/2009 11:55 AM
Para Rui Faria <rui.faria at upf.edu>
Cc Jason Stajich <jason at bioperl.org>; sandraneto_ at hotmail.com; bioperl-l List <bioperl-l at lists.open-bio.org>
Asunto Re: question about a PAML module

Hi Rui and Sandra,

Could you file this as a bug report at 



Once you've created the bug report with a brief description of the problem and submitted it, please attach the following to the bug report:
- sample input files (a sequence file and a tree file, probably)
- a script which reproduces the problem
- the output (error messages) like you show below

When I updated the code to work with the current version, I didn't exhaustively test all of the different modes of running codeml, so I appreciate you reporting this.

There was another, similar issue reported a few days ago. I will try to take a look at both of these bug reports soon.


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