CLARK@GALEN.OCI.UTORONTO.CA (06/30/91)
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@bchs.uh.edu (Dan Davison) and netserv@embl.bitnet or netserv@embl-heidelberg.de (Rainer Fuchs). Steve Clark clark@galen.oci.utoronto.ca (Internet) clark@utoroci (NetNorth/Bitnet)