[BiO BB] clustalw

Roy Chaudhuri roy at colibase.bham.ac.uk
Wed Mar 3 07:49:12 EST 2004

> Has anyone used Clustalw in the profile alignment mode? I tried to and found
> that none of the menu items except the first one work. I downloaded the latest
> version (1.83 for DOS) but it seems to have the same problem. If anyone has
> successfully used Clustalw in the profile alignment mode could you please let
> me know how you went about it?

A problem with ClustalW is that error messages sometimes get hidden, as
the menu is redisplayed. I'm guessing there is some problem with your
second profile/sequence set (such as a duplicated sequence name). This
would prevent the second set from loading correctly, and hence disable
the other options. Try scrolling up in your DOS window after attempting
to load the second set, and you should be able to see the error message
and fix the problem. It should say "(loaded)" next to options 1 and 2 if
you have been successful.


Dr. Roy Chaudhuri
Bioinformatics Research Fellow,
Division of Immunity and Infection,
University of Birmingham, UK


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