boxshade 2.7 released

Kay Hofmann khofmann at isrec-sun1.unil.ch
Wed May 25 03:36:37 EST 1994


Dear present (or future?) BOXSHADE users,

I just finished working on a new (and slightly improved) release of this
program. It is used for creating pretty plots from the output of multple
alignment programs. It supports several multiple alignment formats and
several output devices, see below for more details.
The new version (2.7) is for users of DOS, VMS and OSF1 machines.
It is only a minor upgrade compared to 2.6, which was the last release for
DOS machines, but differences to 2.4 (the last version for VMS machines) are
substantial. In addition, the program is now also running on AXP/OSF1
machines, compilation of the source code on ULTRIX should also be possible
but I cannot test it (lacking a pascal compiler for ultrix).

below, I included an excerpt from the documentation:

The most recent version of BOXSHADE is available by FTP from
  vax0.biomed.uni-koeln.de
It is probably also available by FTP from
  ftp.embl-heidelberg.de (very soon)
  ftp.bio.indiana.edu    (at the moment in the Incoming directory)
BOXSHADE 2.7 will also be available by e-mail from netserv at embl-heidelberg.de

-------------------- BOXSHADE  2.7 -----------------------------------

This is a new release of the PASCAL program BOXSHADE , intended for 
shading multiple aligned sequence files.

------------------------------------------------------------------------
What is new in 2.7?
------------------------------------------------------------------------
The new version BOXSHADE 2.7 replaces the previous versions
BOXHADE/DOS 2.6 and BOXSHADE/VMS 2.4

- The biggest difference to the previous versions is important only for
  me as the program author, the user is not supposed to even notice it.
  I restructured the source code in order to use the same code for DOS,
  VMS and OSF1 version. Considered the lacking standardization of PASCAL,
  that turned out to be a major challenge and involved some tricks. The
  implementation-dependent parts are concentrated in a small compilation
  unit, the program source code itself uses only very few conditional
  compilation (which i have to emulate for some of the compilers).

- As a side-effect of this code merging, the new version supports all
  devices and formats of both previous versions. Even if some of them
  are common only in one particular type of environment, they don't hurt
  when using different systems. Supported output devices are now:
  PS, EPS, HPGL, RTF, VT100, ANSI, ReGIS, PC-CRT, DEC-LJ250.

- To take account of the increasing importance of networking, particularly
  of NFS-mounting of remote disks, all version of BOXSHADE can now read
  parameter- and alignment files in both MSDOS and UNIX text file format.
  Unix and MSDOS text files use different line-terminators and PASCAL
  programs usually choke on files having the wrong format. It is now
  possible, for DOS, UNIX and VMS versions of BOXSHADE to share the same
  parameter files. It is also no problem, for BOXSHADE/DOS to read an
  alignment file created by UNIX-Pileup directly from a NFS mounted volume.

- By the new command line paramters /unix and /dos, BOXSHADE can be forced
  to write its output files in either unix or DOS style. If none of the
  flags is used, BOXSHADE writes in the native style of the machine it is 
  running on.

- The new command line parameter /check gives information on all allowed
  command line parameters and allows adding them later. This functionality
  is similar to the GCG programs.

- of all the helpful and important suggestions that unsatisfied users of 
  BOXSHADE sent to me, I picked only a single one for implementing in
  V2.7 (but I promise to include more in V2.8!). When using the option
  of 'shading according to a master sequence', it is now possible to hide
  this master sequence in the final output. By this method, it is possible
  to have more influence on the look of the final alignment graph. For 
  example, it is possible to remove (unconserved) parts of the master
  sequence and thus get shading only in the remaining parts of the
  alignment.

-------------------------------------------------------------------------
 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 2.7 knows about the following input file formats:
 (some of the 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
 + 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 2.7 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





BOXSHADE is completely public-domain and may be passed around and modified
without any notice to the author.

If you have problems, suggestions or remarks, please contact me

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





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