[Bioperl-l] Fwd: program bp_pairwise_kaks

[Jason Stajich]

Markus-

You need to have also installed PAML in order to do the calculation with
PAML.  There is example code on the HOWTOs for running the perl-only Ka/Ks
counts methods that are in Bio::Align::DNAStatistics
Jason Stajich
jason at bioperl.org
http://bioperl.org/wiki/User:Jason


---------- Forwarded message ----------
From: Markus Liebscher <Markus.Liebscher at gmx.de>
Date: Tue, Jan 20, 2009 at 6:22 AM
Subject: program bp_pairwise_kaks
To: jason at bioperl.org


Dear Jason,
I found the Bioperl package very useful. But I failed to run the
bp_pairwise_kaks program.
I tried to run bp_pairwise_kaks as suggested using the command line $
bp_pairwise_kaks.pl -i ../worm_fam_2785.cdna.
The program starts the routine but at the end I get this:

--------------------------------------------------------
CLUSTAL W (1.82) Multiple Sequence Alignments
Sequence format is Pearson
Sequence 1: CBG10100        363 aa
Sequence 2: F22B7.13        525 aa
Sequence 3: C38C10.4        525 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  9
Sequences (1:3) Aligned. Score:  8
Sequences (2:3) Aligned. Score:  96
Guide tree        file created:   [/tmp/5M8igBfS6R/5LbxDi3Xik.dnd]
Start of Multiple Alignment
There are 2 groups
Aligning...
Group 1: Sequences:   2      Score:11215
Group 2:                     Delayed
Sequence:1     Score:2745
Alignment Score 3187
GCG-Alignment file created      [/tmp/5M8igBfS6R/JI0anpGzWn]
cannot remove directory for /tmp/jFAAdGicRB: Directory not empty at
/usr/lib/perl5/site_perl/5.10/Bi
o/Tools/Run/WrapperBase.pm line 243
SEQ1    SEQ2    Ka      Ks      Ka/Ks   PROT_PERCENTID  CDNA_PERCENTID
--------------------------------------------------------

Do you have an idea what happened here and how I can solve this problem? I
appreciate any help with this.
I am running Cygwin under Windows XP, and have installed clustalw, t-coffee,
the bioperl package and the bioperl package run with the "Build" scripts.

Best regards,
Markus.

Dr. Markus Liebscher
Martin-Luther-University Halle/Wittenberg
Dept. Natural product chemistry
Kurt-Mothes-Str.3
06120 Halle (Saale)
Germany