[Bioperl-l] Clustalw && large sequence number

[James Wasmuth]

Sally,

this an alignment package called MAFFT, which I know can cope with a large
number of sequences.  I've run several hundred through (which TCoffee
couldn't cope with), though never 4000.  Anyway have a look...
http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

Unfortunately there's no bioperl module for it yet (when I get time, I
thought I'd "try"), but its command line based so a system call is easy
enough and the results are easy to parse...

Hope this helps...

James



----- Original Message -----
From: "Sally Li" <sallyli97@yahoo.com>
To: <bioperl-l@bioperl.org>
Sent: Thursday, January 16, 2003 8:53 PM
Subject: [Bioperl-l] Clustalw && large sequence number


> Hi,
>
>  I have clustalw run in my Red Hat 8.0 of IBM eServer
>  which has 6 G memory. But I failed to get the
> aligment
> done if sequence number is big, like, 4000 sequences.
>  Any  idea?
>
>  Thank you very much.
>
>  Sally
>
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