*Shading sequence alignments

Dan Jacobson danj at WELCHGATE.WELCH.JHU.EDU
Wed Mar 18 22:41:17 EST 1992


A request was made for a way to shade residues in a multiple alignment.
Several programs come to mind - the first two are for shading an alignment
which has already been done - no manipulation allowed - these would be
homochart and boxshade.  One of the BEST programs for creating shaded alignments
thing is called MALIGNED and was written by Steve Clark.  Maligned will import
alignments and shade them according to percent identity at each residue
and let you manipulate the alignment, shift sequences, add or delete gaps
etc ... and see how the alignment changes as you manipulate sequences.  You
can also build alignments in Maligned  - it allows you to import upto 199
sequences and build the alignment  manually.  Maligned has many whiz-bang
features including statistics on the alignment.  Maligned only runs on
Vax/VMS systems, but I note that the poster is using VMS NEWS - so they
probably have Vax access.  I asked Steve if he was going to port Maligned to
Unix and he said maybe someday but not to hold my breath :-)

MACAW, written by Greg Schuler et al., is another good program for generating
shaded alignments.  Macaw combines automatic and manual manipulation and
produces nice shaded outputs.  Macaw runs on a PC under windows 3.  The
maximum number of sequences that Macaw can handle is 16.  

Many kudos go to Steve Clark and Greg Schuler for the software and support
as well as to Don Gilbert, Dan Davison and Rob Harper for the bio-ftp
archives (as well as the other ftp sites that have archived these packages).  

Hope this helps,

Dan Jacobson

danj at welchgate.welch.jhu.edu


-------------------------------------------------------------------------
MALIGNED can be obtained by anonymous ftp from:

Host evolution.bchs.uh.edu

    Location: /pub/gene-server/vms
           FILE -rwxr--r--      91152  Mar  3 18:50  maligned.uaa
           FILE -rwxr--r--      91156  Mar  3 18:50  maligned.uab
           FILE -rwxr--r--      91155  Mar  3 18:50  maligned.uac
           FILE -rwxr--r--      21711  Mar  3 18:49  maligned.uad
           FILE -rwxr--r--     294817  Oct 17 00:05  maligned_1_64.uue

Host fly.bio.indiana.edu

    Location: /molbio/vax
      DIRECTORY drwxr-xr-x        512  Oct 31 21:54  maligned
    Location: /molbio/vax/maligned
           FILE -rw-r--r--        358  Aug 13 00:00  maligned.cnf
           FILE -rw-r--r--        747  Jun 23 1991  maligned.com
           FILE -rw-r--r--      48108  Jun 23 1991  maligned.doc
           FILE -r--r--r--      89600  Aug 14 00:00  maligned.exe
           FILE -rw-r--r--       1688  Aug 13 00:00  maligned.hlp
           FILE -rw-r--r--       2401  Jun 23 1991  maligned.readme
           FILE -rw-r--r--     294817  Oct 16 03:35  maligned_1_64.uue
           FILE -rw-r--r--     125546  Aug 13 00:00  maligned_exe.uue
           FILE -rw-r--r--       1809  Jun 23 1991  mouse.maligned
           FILE -rw-r--r--        965  Jun 23 1991  wpmaligned.com

Host nic.funet.fi

    Location: /pub/sci/molbio/vax
           FILE -rw-r--r--     117221  Jan  7 19:44  maligned.zoo



********************************************************************


Macaw can be obtained by anonymous ftp from:


Host aix370.rrz.uni-koeln.de

    Location: /msdos/mswindows3/miscutils
           FILE -rw-rw-r--     115127  Jul 31 1991  macaw103.zip

Host bode.ee.ualberta.ca

    Location: /pub/DOS/win3/util
           FILE -rw-r--r--     194322  Jun  6 1991  macaw.zip
           FILE -rw-r--r--     115127  Feb 24 20:26  macaw103.zip

Host cica.cica.indiana.edu

    Location: /pub/pc/win3/util
           FILE -rw-r--r--     115127  Aug 15 00:00  macaw103.zip

Host cs.dal.ca

    Location: /pub/comp.archives
      DIRECTORY drwxrwxrwx        512  Apr  1 1991  macaw

Host du9ds3.uni-duisburg.de

    Location: /pub/msdos/win3/util
           FILE -r--r--r--     194322  Jun  1 1991  macaw.zip

Host evolution.bchs.uh.edu

    Location: /pub/gene-server/incoming
           FILE -rwxr--r--     115127  Aug 15 00:00  macaw103.zip

Host fly.bio.indiana.edu

    Location: /molbio/ncbi
           FILE -rw-r--r--       1504  May 14 1991  readme.macaw

Host ftp.uni-kl.de

    Location: /pub/bio
      DIRECTORY drwxr-xr-x        512  Aug 20 00:00  macaw
    Location: /pub/bio/macaw
           FILE -rw-r--r--     115127  Aug 20 00:00  macaw103.zip

Host gatekeeper.dec.com

    Location: /.2/micro/msdos/win3/util
           FILE -r--r--r--     194322  Jul 19 1991  macaw.zip

Host mbio.med.upenn.edu

    Location: /pub
           FILE -rw-r--r--      32115  Apr  9 1991  macaw-tutorial.zoo
           FILE -rw-r--r--     136501  Apr  9 1991  macaw100.zoo
           FILE -rw-rw-r--     149572  Jan 31 00:01  macaw103.zoo

Host monu6.cc.monash.edu.au

    Location: /pub/Win3.0/util
           FILE -rw-rw-r--     115127  Aug 21 00:00  macaw103.zip

Host ncbi.nlm.nih.gov

    Location: /pub
      DIRECTORY drwxr-xr-x        512  Oct 25 20:10  macaw
    Location: /pub/macaw
           FILE -rw-r--r--     148594  Jul 31 1991  macaw103.arc
           FILE -rw-r--r--     115808  Jul 31 1991  macaw103.lzh
           FILE -rw-r--r--     115127  Jul 31 1991  macaw103.zip
           FILE -rw-r--r--     149572  Jul 31 1991  macaw103.zoo

Host nic.funet.fi

    Location: /pub/msdos/windows/util
           FILE -rw-r--r--     115802  Aug 23 00:00  macaw103.lzh

Host puffin.doc.ic.ac.uk

    Location: /ibmpc/windows3/util
           FILE -r--r--r--     194322  Apr 15 1991  macaw.zip
           FILE -r--r--r--     115127  Aug 15 00:00  macaw103.zip

Host uhunix2.uhcc.hawaii.edu

    Location: /pub/ibmpc/win3/util
           FILE -rw-r--r--     115127  Jan 18 02:00  macaw103.zip

Host wuarchive.wustl.edu

    Location: /mirrors2/win3/util
           FILE -r--r--r--     115127  Aug 14 00:00  macaw103.zip




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