*Announce* BOXSHADE v3.2 available

[Unknown]

**************************ANNOUNCEMENT**********************************
*                                                                      *
*                     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.


------------------------BOXSHADE v3.2--------------------------------

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 
shading).
*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 
residues printed. 

-------------------------------------------------------------------------
 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 
itself,
it has to take as input a file preprocessed by a multiple alignment 
program
or a multiple file editor. See below for a list of supported input 
formats
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 
to
supply the program with parameters from the command line.
At the moment, the VMS and DOS versions of BOXSHADE have identical user
interfaces.


- 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 
work
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 
Laserprinter
    or for further conversion with a POSTCRIPT interpreter (like 
GHOSTSCRIPT)
  + HPGL for export to various graphics programs or for 
conversion/printing
    with the shareware program PRINTGL. Plotting BOXSHADE output on a 
plotter
    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 
depend
    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 
has 
    to be loaded in CONFIG.SYS previously. Possible character renditions 
are 
    reverse, bold,underlined, blinking etc. On non-DOS systems, this 
option
    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 
emulator. 
  + 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 
a 
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. 

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

PROGRAM AVAILABILITY:

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 
help?) 

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... 


Kay Hofmann
Bioinformatics group
ISREC
CH-1066 Epalinges s/Lausanne
Switzerland
E-mail: khofmann at isrec-sun1.unil.ch

Michael D. Baron
Institute for Animal Health
Ash Road
Pirbright
Surrey GU24 0NF
U.K.
E-mail: michael.baron at bbsrc.ac.uk