[Bioperl-l] PAML wrappers

[Albert Vilella]

Hi Sergios,

(I forward your email to the bioperl mailing list)

> i noticed there are wrappers for the ctl's of PAML's codeml. do u  
> have for baseml, too? do u have them tested on OSX? can u email them  
> to me, pls? zip them, preferably (no compression).
> 

The wrappers you mention are part of bioperl-run. They should work under
OSX having bioperl installed:

Download http://bioperl.org/DIST/current_core_unstable.zip
Download http://bioperl.org/DIST/current_run_unstable.zip

unzip current_run_unstable.zip
unzip current_core_unstable.zip
export PERL5LIB="$HOME/bioperl-1.5.1:$HOME/bioperl-run-1.5.1"

tar zxf paml3.14b.OSX_G5.tar.gz
export PAMLDIR="$HOME/paml3.14/src"
cd $PAMLDIR
make

-----

I believe that the codeml wrapper is the most tested and used, but the
baseml wrapper has a problem right now with the input files:

PAML's baseml is pickier than a hungry three year old in an expensive
French bistro about the format of the sequence file and the tree file,
so the example in the synopsis for
bioperl-run-1.5.1/Bio/Tools/Run/Phylo/PAML/Baseml.pm is not working
right now (at least for me).

You will find more information on how to run PAML wrappers in the 
documentation. For example, in this howto:

http://bioperl.org/HOWTOs/html/PAML.html

Cheers,

    Albert.