[Bioperl-l] Bio::TreeIO

Olena Morozova olenka.m at gmail.com
Thu Feb 9 17:49:48 EST 2006


Hi all,

Probably a very stupid question, but the get_lca function does not
work for unrooted trees, does it?
I am trying to get the LCA for a set of nodes in a phylip tree, and I
am using the script in the HOWTO.
Thanks,
Olena

On 2/8/06, Hubert Prielinger <hubert.prielinger at gmx.at> wrote:
> Hi,
> If I want to parse a Blast Output (Version 2.2.12) with Bio::SearchIO,
> I get the following error message:
>
> MSG: no data for midline Query  1   WWWKWRW  7
> STACK Bio::SearchIO::blast::next_result
> /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1151
> STACK toplevel
> /home/Hubert/installed/eclipse/workspace/Database_Search/Blast.pl:21
>
> is that a bug......
>
> If I want to parse Blast Output (version 2.2.13), I don't get anything.....
> I'm using bioperl 1.4
>
> before, I have installed bioperl 1.4, it worked fine parsing Blast
> Output (version 2.2.12), but I don't remember which bioperl version I
> had installed
>
> thanks in advance
>
> Hubert
>
>
>
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