protein seq. alignment programe

Dan Jacobson danj at WELCHGATE.WELCH.JHU.EDU
Fri Dec 18 17:14:45 EST 1992

In article <9212180511.AA27010 at> vrati at (Sudhanshu Vrati) writes:
>I am trying to align more than three protein sequences using gcg pile up
>programe.  Are there any other programes available for this purpose ?
>Thanks for your response,

Yes there are several programs that help you do multiple alignments here 
are a three of them - ClustalV, Treealign, and Macaw.

Clustal(V) is a popular aligner that is available for Unix, VMS, DOS, and
Macs.  You can get it by anonymous ftp from several places I'll list one here:


    Location: /pub/gene-server/dos
           FILE -rwxr--r--      91153  Sep 16 1991  clustalv.uaa
           FILE -rwxr--r--      91156  Sep 16 1991  clustalv.uab
           FILE -rwxr--r--      91156  Sep 16 1991  clustalv.uac
           FILE -rwxr--r--       6241  Sep 16 1991  clustalv.uad
    Location: /pub/gene-server/incoming
           FILE -rw-r--r--     199453  Sep 13 03:54  clustalv.exe
    Location: /pub/gene-server/mac
           FILE -rwxr--r--      97223  Sep 16 1991  clustalv1.hqx
           FILE -rwxr--r--      66491  Sep 16 1991  clustalv2.hqx
    Location: /pub/gene-server/unix
           FILE -rwxr--r--      91155  Sep 16 1991  clustalv.uaa
           FILE -rwxr--r--      30012  Sep 16 1991  clustalv.uab
    Location: /pub/gene-server/vms
           FILE -rwxr--r--      91154  Sep 16 1991  clustalv.uaa
           FILE -rwxr--r--      44054  Sep 16 1991  clustalv.uab

Treealign is another alignment package which is available for Unix
and VMS.  It too is available by anonymous ftp from several places - one is:


    Location: /molbio/align
           FILE -rw-r--r--     298974  Jun 17 1991  treealign.shar

Macaw is an alignment package (can do up to 16 sequences at a time) for the 
PC with Windows 3 (or higher), you can obtain it by anonymous ftp from:


    Location: /pub
      DIRECTORY drwxr-xr-x        512  Sep  1 20:41  macaw
    Location: /pub/macaw
    Location: /pub/macaw/util/.source
         FILE -rw-r--r--  1 1028       269238 Jul 14 21:38 macaw105.zoo
         FILE -rw-r--r--  1 1028       133876 Dec 18 16:56 macaw106.arc
         FILE -rw-r--r--  1 1028       104406 Dec 18 16:56 macaw106.lzh
         FILE -rw-r--r--  1 1028       104536 Dec 18 16:56
         FILE -rw-r--r--  1 1028       134642 Dec 18 16:56 macaw106.zoo

If you get Macaw you'll probably want to get a (hardcopy) manual which
Greg Schuler will send you if you drop him a note (schuler at

Kudos go to the authors and the ftp site providers.    

Best of luck,

Dan Jacobson

danj at

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