[Bioperl-l] Script to Calculate Pairwise Ka,Ks

Jason Stajich jason at bioperl.org
Mon Jun 14 14:48:11 EDT 2010

I think you can also just add that clustal dir in your PATH.

I'm fwding to bioperl list for help as I don't have time to debug right 
now, sorry.


Haktan Suren wrote, On 6/14/10 1:50 PM:
> Dear Jason Stajich,
> First of all, I would like to thank you for the great script that you 
> wrote. However I wasn't able to run it because it gives me the 
> fallowing error. I have looked into web but haven't found the solution 
> yet. I appreciate if you could provide me any kind of help.
> The error is
> Could not find the executable for clustalw, make sure you have 
> installed it and have either set CLUSTALWDIR or it is in your PATH at 
> kaks2.pl <http://kaks2.pl> line 108.
> For your information, I have downloaded clustalw-2.0.12-macosx.dmg 
> <http://www.clustal.org/download/current/clustalw-2.0.12-macosx.dmg> 
> from http://www.clustal.org/download/current/ and pointed this 
> software at the very beginning of the code like
> '/Users/hsuren/Downloads/BioPerl-1.6.1/Bio/Tools/Run/Alignment/clustalw/clustalw2/' 
> }
> But it still gives me the same error. I am attaching the perl script 
> as well incase you need.
> ------------------------------------------------------------------------
> Best Regards,
> Haktan Suren

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