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
