[Bioperl-l] All-vs-all BLAST

[James Wasmuth]

The documentation for TCoffee and Clustalw are not available through 
docs 1.4. Though I'll stand corrected.

try:
http://doc.bioperl.org/releases/bioperl-1.0.2/Bio/Tools/Run/Alignment/Clustalw.html

-james

Paulo Almeida wrote:

> Hi,
>
> You want to compare all the possible pairs of sequences in the set? If 
> that is it, you can try putting all the sequences in an array, blast 
> the first against all the others, shift it out of the array and then 
> repeat the process until the array is empty. If it's a multiple 
> alignment you want, you could probably use 
> Bio::Tools::Run::Alignment::Clustalw 
> <http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/Alignment/Clustalw.html> 
> (I was going to link to the webpage, but that link is broken in the 
> Bioperl webpage).
>
> -Paulo
>
> Peter J Stogios wrote:
>
>> Hello,
>>
>> I'm looking for a script to do an all-vs-all BLAST comparison of a 
>> set of sequences.
>
>
>
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