clustalw question...

[Fernan Aguero]

+----[ Vasudevan, Geetha <gvasudevan at medarex.com> (15.Jul.2003 15:09):
|
| Do you know which option to use? Thanks.

Most of the time i run clustalw interactively (i.e. without
passing options in the command-line. In this way, I choose
option 1 (sequence input), then 2 (MSA), then 9 (output
format), then again 9 (toggle output order).

The toggle switches between 'aligned' and 'input file'. The
last one is the one you want.

If you run it non-interactively you need:
-OUTORDER=   :INPUT or ALIGNED
(output from calling 'clustalw -help')

Hope this helps,

Fernan

| 
| 
| -----Original Message-----
| From: Fernan Aguero [mailto:fernan at iib.unsam.edu.ar] 
| Sent: Tuesday, July 15, 2003 11:04 AM
| To: Vasudevan, Geetha
| Subject: Re: clustalw question...
| 
| +----[ Vasudevan, Geetha <gvasudevan at medarex.com> (15.Jul.2003 14:38):
| |
| |    Is it possible to force the order of alignment in clustalw? I would
| |    like the first seq in the fasta file to be on top.
| |
| +----]
| 
| Yes you can. In clustalw, you can set the order of sequences
| to be the same of the input file.
| 
| Fernan
| 
| -- 
| F e r n a n   A g u e r o
| http://genoma.unsam.edu.ar/~fernan
| 
|
+----]

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan