*Announce* BOXSHADE v3.2 available
Tue Apr 16 06:24:29 EST 1996
* BOXSHADE version 3.2 *
A new version of BOXSHADE, the PASCAL program intended for
shading multiple aligned sequence files, is now available from the EMBL
software archive. The upgrade to version 3 was never properly announced,
so the following details, extracted from the documentation
(BOXSHAD3.DOC), are to bring us up to date.
The major change is the addition of PICT file output. PICT files are
standard on Macs, and are also read by most of the PC drawing packages
(e.g. Corel, Harvard Graphics, FreeLance for Windows). The files have
been tested on every Mac and PC program I could get my hands on, and
import correctly. Extra notation, outlining regions, etc., can now be
done to the shaded alignment, which can also be in colour (text and
*Nothing* is perfect in this world, however, and an editable figure
containing (for 6 sequences of 300 amino acids each) about 4000
editable objects will give most computers a headache unless they are
very fast and have buckets of free RAM. The image that is imported is
'grouped', and can be moved around and sized, and things put over or
behind it. If you 'ungroup' it, you will have problems. Be warned!!
Partly because of this problem, I have included the option of
'printing' either the shading *only*, or both shading and text. The
text alone, without modification, can be produced using the ASCII file
output option, or with PRETTY or other programs. This can be put on
top of the shading. The shading can be resized to fit the text, as
required. This procedure gives you less than half the number of
'objects', and makes everything quicker.
A few other small things have been tidied up: the 'master' sequence
can be set in the command line for 'comparison to a single sequence,
and /split is enforced for EPSF and PICT output. I tried to take care
of the situation where the block is bigger than the page (anyone out
there aligning 100 sequences?). Note that the program will still allow
you to put too many characters on the page for PS, EPSF, HPGL, FIG and
PICT output, where different font sizes are possible, but, hey, we're
all intelligent people, right?
-------------------- BOXSHADE 3.0 -----------------------------------
This is version 3.0 rather than 2.8 because the shading algorithm has
been completely rewritten, and is now more sophisticated. Basically,
MDB wrote it to do what he would do if he was shading an alignment by
hand. As an unsophisticated molecular biologist, he hopes it will meet
the requirement of all the other unsophisticated molecular biologists
out there. The full description of the shading process is below.
Also in this version, the introduction of a 'threshold' fraction of
residues that must agree before there is a consensus at that position.
Two more output formats have been included. These are a .FIX file for
the Unix program xfig, and ASCII text output, with varying or conserved
SHORT PROGRAM DESCRIPTION
- Purpose -
BOXSHADE is a program for creating good looking printouts from multiple-
aligned protein or DNA sequences. The program does no alignment by
it has to take as input a file preprocessed by a multiple alignment
or a multiple file editor. See below for a list of supported input
and output devices.
In the standard BOXSHADE output, identical and similar residues in the
multiple-alignment chart are represented by different colors or shadings.
There are some more options concerning the kind of shading to be applied,
sequence numbering, consensus output and so on.
The user interface is a bit clumsy at the moment, one has to answer a lot
of questions in order to get the desired output. There is, however, the
possibility to use default parameters from a standard parameter file or
supply the program with parameters from the command line.
At the moment, the VMS and DOS versions of BOXSHADE have identical user
- Input formats -
BOXSHADE 3.2 knows about the following input file formats:
(some of them are generally used only for MSDOS or VMS systems)
+ CLUSTAL and CLUSTALV, multiple alignment program, DOS/VMS/MAC
default extension .ALN
+ ESEE, multiple sequence editor, DOS
default extension .ESE
+ PHYLIP, phylogenetic analysis package, DOS, VMS, UNIX
default extension .PHY
+ PILEUP and PRETTY of the GCG sequence analysis package VMS/UNIX
default extensions .MSF and .PRE
NB!! you are strongly encouraged NOT to use the PRETTY format as
input, it may be incompatible with the revised version of .MSF input.
We can't actually think why anyone would use this format now, .MSF
files are more useful generally.
+ MALIGNED, multiple sequence editor, VMS only
default extension .MAL
BOXSHADE tries to determine the file type from the extension but will
also if different extensions are used.
- Output devices -
BOXSHADE 3.2 supports the following output devices
+ POSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on a
or for further conversion with a POSTCRIPT interpreter (like
+ HPGL for export to various graphics programs or for
with the shareware program PRINTGL. Plotting BOXSHADE output on a
is generally not recommended
+ RTF for export to various word-processing and graphics programs
+ CRT, uses direct screen writes to the PC-monitor. Possible options
on the graphics adapter used. This output device is supported only in
the MSDOS version.
+ ANSI. On a PC, this option uses an ANSI device driver (ANSI.SYS) that
to be loaded in CONFIG.SYS previously. Possible character renditions
reverse, bold,underlined, blinking etc. On non-DOS systems, this
behaves more or less like the VT100 output mode.
+ VT100 for display on a VT100 compatible terminal or emulator.
+ ReGISterm for display on a ReGIS compatible graphics terminal or
+ ReGISfile for later conversion by the program RETOS (copyright DEC)
in order to print on DIGITALs printer series.
+ LJ250 for printing on DIGITALS LJ250 color printer.
+ ASCII output showing either the conserved residues or the varying
ones (others as '-').
+ FIX file for xfig 2.1.
+ PICT file for MAC and PCs
- Shading strategies (similarity to consensus or single sequence) -
Starting with version 3, BOXSHADE has a new shading system. The first
difference is the introduction of a threshold fraction of residues
that must agree for there to be a consensus. Previously, the program
assumed that SOME residue was always the consensus. If no two residues
were the same, the first sequence provided the consensus residue. The
threshold fraction can be any number between 0.0 and 1.0. The number
of sequences that must agree for there to be a consensus is, as you
might expect, this fraction times the total number of sequences in the
alignment (fractions of a sequence count as one, e.g. 3.2 becomes 4).
The second difference is the idea of 'consensus by similarity'; this
tries to take account of the situations where all the sequences may
have (for example) R or K at a position, but neither in a majority. It
would not be logical to shade one type of residue as 'identical'
and the other as 'similar'; the threshold function might also
eliminate both as being in too small numbers. Therefore, if there is not
single residue that is conserved (greater than the threshold) at a
position, the program looks for a 'group' of amino acids that fulfills
the requirements. 'Groups' are defined in the .grp files. Users can
tailor these to their personal prejudices. Any amino acid not listed
is assumed not to be in a group.
The full source is distributed with the archive. Anyone is welcome
(indeed encouraged!) to recompile this for other platforms. Executables
are available for VAX/VMS (boxshad3.uue in the VAX subdirectory) and
AXP/OSF1 (box_exe_axposf1.tar.Z in the unix subdirectory). Peter A.
Stockwell (peter at sanger.otago.ac.nz) has ported it to DEC's Ultrix 4.4
and Sun/Solaris 2.3. There is a DOS executable of version 3.0 in the DOS
subdirectory of the EMBL archive (Sorry, we *don't* have facilities to
make new compiled DOS versions. Anyone out there with TurboPascal care to
The program can also be run from ISREC's web page. The URL for the
boxshade server is under http://ulrec3.unil.ch/software
The number of options available via WWW is somewhat reduced, not only
to make things simpler, but mainly since the WWW forms interface does not
offer conditional menus.
Maybe one day someone will write a Java version...
CH-1066 Epalinges s/Lausanne
E-mail: khofmann at isrec-sun1.unil.ch
Michael D. Baron
Institute for Animal Health
Surrey GU24 0NF
E-mail: michael.baron at bbsrc.ac.uk
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