Multiple sequence alignment editor available

Sat Jun 29 13:49:27 EST 1991

	I have recently deposited in several archives a multiple sequence 
alignment editor, called MALIGNED, that runs in a VAX/VMS environment. Up 
to 199 sequences can be aligned. What follows is a brief summary of some of
its features. 

	Most importantly, the sequences in the alignment are highlighted 
on the screen to show where they match, and the highlighting is updated 
every time a change is made in the alignment. This makes it easy to judge 
the effect of changing the alignment by eyeballing the overall amount of 
highlighting on the screen. Up to three styles of highlighting can be used 
at once, such as bold, reverse, boldreverse, blink, etc, plus normal 
display, so altogether four levels of matching can be seen. Also, 
there are four ways the matches can be calculated. In Conserved mode, 
different levels of matching, called stringencies, have different styles of 
highlighting. The default is set to 100%, 80-99%, 60-79% and <60% 
identical, but these can be set to any values. Quantify mode highlights the 
three most common characters in each column in different styles, and 
Differences mode displays the top sequence in full; the ones below it are 
displayed as dots "." where they are the same as the top sequence, or the 
actual sequence character where they are different. Finally, Lineup mode 
doesn't highlight anything but has a very quick screen update time. (This 
is not to imply that the other modes are pokey, but it is noticible when 
working over a modem.)

	MALIGNED provides the option to display a 'consensus' sequence, and
several groups of characters can be set to be treated as if they were
identical (for example, Lysine and Arginine). It imports alignments from
the GCG Lineup and Pileup programs and exports Lineup alignments. It also
can create a file providing various statistics on all pairs of sequences in
the alignment (% identical, % gaps, etc), and can generate a file that can
be used as input for Joe Felsenstein's phylogeny programs in his Phylip
package. There are a number of other features as well. 

	All options, including highlighting styles on the screen and for 
the printer, can be chosen from within the program. MALIGNED can be 
configured to work with any device that uses escape codes to change the 
display style. This includes but is not limited to all DEC VT series 
terminals, compatibles and emulators, Hewlett Packard LaserJet printers 
and compatibles, and dot-matrix printers. Sample configuration files are 
included for the HP LaserJet series II and Epson 9-pin dot-matrix 
printers, as well as instructions on how to modify these or make your own.

	Because MALIGNED is an alignment editor and not a sequence editor, 
it will not allow you to change the actual sequence, aside from adding gaps 
or cutting off the ends. This is to prevent accidental mutations that can 
be very difficult to discover.

	MALIGNED is available from a number of sources. By FTP:
menudo.uh.edu (thanks to Dan Davison), ftp.bio.indiana.edu (ditto to Don
Gilbert), and nic.funet.fi (Rob Harper). By mail server:
gene-server at bchs.uh.edu (Dan Davison) and netserv at embl.bitnet or
netserv at embl-heidelberg.de (Rainer Fuchs). 

Steve Clark

clark at galen.oci.utoronto.ca    (Internet)
clark at utoroci                  (NetNorth/Bitnet)

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