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)
