HELP wanted: alignment programs?

[Dan Jacobson x-8453]

Bruce Ramsey writes:

>I would like some information on sequence alignment
>programs.  Specifically, I've been using Multalin to
>align short, newly-sequenced DNA stretches to a much
>larger consensus sequence.  I'm told that Multalin is
>not the program of choice for doing this, and that perhaps
>"R-Align" (spelling?) would be better.
>
>Could someone direct me to an appropriate ftp server 
>address for this program, or instead recommend something
>different?
>
>I would prefer it to be DOS-based (not out of choice, but
>because that's what we've got - DOS machines).  

There is an ralign.c at ftp.bio.inidana.edu

/molbio/align

ralign.c

Note that all the required files seem to be concatenated together in this one
entry.

As to other programs for MSDOS - well if you have Windows 3.0 or higher
and are doing multiple alignments you might want to take a look at MACAW.
ClustalV also comes to mind as a good multiple alignment program which will
run on a PC.

There are a number of programs which will align just two sequences.


Macaw is available from many places but its home (and latest updates) is at
NCBI.

Host ncbi.nlm.nih.gov

    Location: /pub
      DIRECTORY drwxr-xr-x        512  Apr 20 21:25  macaw
    Location: /pub/macaw
           FILE -rw-r--r--     156669  Apr 20 21:25  macaw104.arc
           FILE -rw-r--r--     122103  Apr 20 21:25  macaw104.lzh
           FILE -rw-r--r--     121798  Apr 20 21:25  macaw104.zip
           FILE -rw-r--r--     311764  Apr 20 21:25  macaw104.zoo



------------------


Clustalv is available from several sites, I'll list two here:

Host evolution.bchs.uh.edu

    Location: /pub/gene-server/dos
           FILE -rw-r--r--      91153  Sep 16 18:11  clustalv.uaa
           FILE -rw-r--r--      91156  Sep 16 18:11  clustalv.uab
           FILE -rw-r--r--      91156  Sep 16 18:11  clustalv.uac
           FILE -rw-r--r--       6241  Sep 16 18:11  clustalv.uad


Host fly.bio.indiana.edu

    Location: /molbio/align
           FILE -rw-r--r--       2079  Sep  5 12:51  clustalv.note
           FILE -rw-r--r--       5060  Sep  1 13:21  clustalv.readme
           FILE -rw-r--r--      86385  Sep  6 21:43  clustalv.tar.Z


------------------------

Kudos go to the authors and archivers.

Hope this helps,

Dan Jacobson

danj at welchgate.welch.jhu.edu