***ANNOUNCEMENT***** January 1999
MACBOXSHADE version 2.15 is now available from the BOXSHADE web page:
http://www.isrec.isb-sib.ch/sib-isrec/boxshade/MacBoxshade/MacBoxshade
2.15.hqx
It sould be available also from the iubio archive:
http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/mac/macboxshade215.hqx
MACBOXSHADE is a program for creating good-looking printouts from
multiple aligned
protein or DNA sequences. The program does no alignment by itself, it
has to take
as input a file preprocessed by a multiple alignment program or a
multiple file editor.
Input format: GCG-type MSF file
Output formats: ASCII, RTF, PostScript, EPSF and PICT as files; ASCII
and PICT
display on screen.
Output options: shade/colour by consensus or residue type; consensus
line;
ruler line; sequence numbering at either end of the line(or both);
identity/similarity matrix; user control of residue groups; user control
of colours and case of letters at four
levels of conservation or nine different residue types.
NEW in version 2.15:
This version is purely a bug-fix, in response to a couple of
complaints/requests, or
things I had noticed.
1) fixes a minor problem with the appearance of the dialog for entering
sequence start
numbers, and allows one to use the TAB and SHIFT-TAB keys to move down
and up the list
(respectively); fixes a memory leak associated with this dialog.
2) the program should now accept sequence names with any imaginable
printable character
in them (except SPACE, which is not allowed in GCG, either).
3) the program should now correctly handle RNA sequences (mea culpa,that
I never
checked). The program considers T and U to be in the same group always:
if you are
doing protein alignments, this should not be a problem, as I believe
that there is no
aa code U. If you have a mixed RNA/DNA alignment, however, it will not
score U=T. If
anyone actually does such things, and finds this a problem, let me know.
4) The program now comes with an alternate version, 2.xxE, the E being
for Executor.
Executor is a Mac emulator for DOS, Windows and Unix, and I had to make
some mods to
the program to get it to run without crashing under the emulator. The
pict display
isn't particularly nice under Executor, as Executor does not correctly
emulate
DrawString (at least, the DEMO version doesn't); however, the PICT files
it generates
seem to be kosher. The dialog to select sequence start-numbers crashes
Executor, but
Ardi (the makers of Executor) haven't replied to my request for the
meaning of the
error codes produced. If you don't need this version, throw it away.
5) A minor bug in the appearance of the help window has been fixed.
6) fixes a bug in the Landscape option for Postscript files that was
clipping off
the top of the alignment.
As always, please send any reports of bugs or other problems with
MacBoxshade to:
Michael D. Baron Ph.D. E-mail: michael.baron at bbsrc.ac.uk
Institute for Animal Health
Ash Road
Pirbright
Surrey GU24 0NF
U.K.
