[Bioperl-l] hacked version of PHYLIP

[Jason Stajich]

On Fri, 8 Nov 2002, nkuipers wrote:

> Hello all,
>
> Was idly browsing through the documentation of bioperl modules of interest.
> In Bio::AlignIO::phylip, the synopsis code includes the following:
>
> #you can set the name length to something other than the default 10
> #if you use a version of phylip (hacked) that accepts ids > 10
> my $phylipstream = new Bio::AlignIO(-format => 'phylip', -fh   => \*STDOUT,
> -idlength=>30);
>
> Might one of you know where to find such a version?
>

You just need to recompile phylip with new default length parameters for
IDs

% grep "define nmlngth" *.c
In you phylip src dir will show you all the lines you would need to
fix.

A simple perl/sed cmd for the replacement should get you going.


> Thanks,
>
> Nathanael Kuipers
> ---
> Center for Biomedical Research,
> Dept.of Biology,
> University of Victoria
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu