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Request recommendation on sequence alignment program.

Thomas Sicheritz Thomas.Sicheritz at molbio.uu.se
Fri Nov 14 22:38:06 EST 1997

Sebastian Bassi <sbassi at cairp.org> writes:

>   I want a recommendation for a program to do nucleotide or amino acid
>   sequence  alignment.  I  want  this  for taking the output to PHYLIP
>   package for making a tree.
>   The main characteristics I'd like to see on the program are:
>   -for PC (DOS/WIN).
>   -Shareware or freeware.
>   -complete documentation.
>   Here  are  the programs mentioned on PHYLIP documentation for making
>   sequence alignment:
>   VOSTORG, TreeAlign, ClustalW and MALIGN.
>   Witch one do you recommend me?

Definitely clustalW.
* you can use the same program on different platforms (Unix, PC, Mac ...)
* its relatively fast
* there are plenty of tutorials available on the net
* you can run it on the web to http://www2.ebi.ac.uk/clustalw/


Sicheritz Ponten Thomas E.              UPPSALA UNIVERSITY 
Vaksalagatan 29C S-753 31 Uppsala       Biomedical Center
Home: +46 18  129021                    Department of Molecular Biology
BMC:  +46 18 4714214                    BOX 590 S-751 24 UPPSALA Sweden
Fax   +46 18  557723                    http://evolution.bmc.uu.se/~thomas
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