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##
## README FOR GFF2APLOT v2.0
##
##
## $Id: README,v 1.1 2003/03/17 17:58:46 jabril Exp $
##

  Dear User:

    This file contains important program information. Please read
  these tips through carefully, before beginning to work with GFF2APLOT.
  See INSTALL file for further tips on how to install the program
  and related scripts on your system.


-------------------------------------------------------------------------------
  License Terms
-------------------------------------------------------------------------------

    GFF2APLOT v2.0

    a program to visualize the alignment of two genomic sequences
    together with their annotations. From GFF-format input files
    it produces PostScript figures for that alignment.
    

      Copyright (C) 1999-2003 - Josep Francesc ABRIL FERRANDO
                                        Thomas WIEHE
                                       Roderic GUIGO SERRA

  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version (http://www.gnu.org).

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program; if not, write to the Free Software
  Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.


-------------------------------------------------------------------------------
  Author's Address
-------------------------------------------------------------------------------

    Josep Francesc ABRIL FERRANDO

      GENOME BIOINFORMATICS LAB
      GRIB --- IMIM / UPF / CRG
      Passeig Maritim de la Barceloneta, 37-49.
      08003 - Barcelona, Catalonia, Spain.

       Phone:  +34 93 2240302
         Fax:  +34 93 2240875

      e-mail:  jabril@imim.es
         URL:  http://genome.imim.es/~jabril


-------------------------------------------------------------------------------
  Listing Files for Current Distribution
-------------------------------------------------------------------------------

  You can retrieve the latests files from the following FTP address:

      ftp://genome.imim.es/pub/gff_tools/gff2aplot/

  The current distribution tarball contains the following files
  and subdirectories:

  README                 This file...

  GNU-GPL                The GNU General Public License Version 2.

  INSTALL                Instructions on how to prepare 
                         the GFF2APLOT scripts to run them
                         in your system.
                         Please, take a look at it...

  Makefile               Well, you know... ;^D

  src/
                         GFF2APLOT and related scripts.

    src/gff2aplot.pl
                         The main program, which converts GFF input
                         into alignment PostScript plots.
    src/parseblast.pl
                         A parser for the standard output
                         from most of the BLAST programs available
                         (NCBI-Blast/WashU-Blast/WebBlast/MegaBlast).
    src/blat2gff.pl
                         Filtering BLAT output into GFF.
    src/sim2gff.pl
                         Converting SIM output into GFF.
    src/ali2gff
                         C program that parses SIM/Mummer output
                         and produces GFF records for the alignment.

  bin/
                         It is empty until you make
                         the executables for the distribution.

  doc/
                         Contains documentation for gff2aplot,
                         initially the "User's Manual".

  examples/              A set of three examples,
                         in separate directories, each containing
                         GFF data, customization files and
                         PostScript output obtained with gff2aplot.
                         See the corresponding README file to see
                         how the figures were generated.
    examples/wublast/
    examples/mhcregion/
    examples/splice_sites/


-------------------------------------------------------------------------------
  Reporting Bugs and Suggestions
-------------------------------------------------------------------------------

  + GFF2APLOT author's e-mail adress: jabril@imim.es


  + HELP:

  If you need help after reading manual pages you are free to send an e-mail
  to authors. It will help to filter your mail properly if you start your 
  subject string with "[GFF2APLOT] HELP:".

  You will get a reply as soon as possible.


  + BUGS:

  If you find any bug or something is not plotted properly, you can send a bug
  report which subject string may start with "[GFF2APLOT] BUG:".


  + SUGGESTIONS:

  We thank any helpful suggestion for improving our program. Message
  subject string will start with "[GFF2APLOT] SUGGEST:".


-------------------------------------------------------------------------------
  Acknowledgements
-------------------------------------------------------------------------------

  We would like to thank Matthias Platzer, at IMB, Jena, for helpful
  comments while developing the program prototype. We would like to
  thank the colleagues at Genome Bioinformatics Lab within the GRIB
  for their extensive testing of GFF2APLOT.

  We would also thank users that will cite the paper on GFF2APLOT, 
  or at least it's web-site URL. Paper is currently submitted,
  so you may cite GFF2APLOT as:

	  http://genome.imim.es/software/gfftools/GFF2APLOT.html

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