HTML4BLAST - v1.6

html4blast is a simple hypertext Blast output formatter. It provides
links to retrieve databanks entries from their accessions numbers,
names, via www servers; and if wanted, an alignment summary image.

Synopsis:
usage: html4blast [options] <file>

options [default]:
  -e        ... External databases links.
  -g        ... Make graphical alignment summary.
  -h        ... Prints usage display and exit.
  -l        ... Draw one HSP per line (require -g).
  -n        ... No databases links.
  -o <file> ... Set output to <file> [blast.html].
  -s        ... Srs databases links.

Example: html4blast -sg test/ncbi2.blast
This command line produce a HTML file blast.html containing an image and
links for SRS databases queries.

By default, databases links use efetch retrieval system. If many flags are
set together, is uses the following order:
	1) No databases links.
	2) External sites (accession number only).
	3) Sequence Retrievial System (SRS).
	4) Efetch queries [default].

Available databases links by retrieval system:
Efetch (default) ... Accession, Locus/Id
Srs (-s)         ... Accession, Locus/Id
Extern (-e)      ... Accession, Gi

Availables databases and www servers can be easily configured respectivly
in html4blastrc system file, then in .html4blastrc for user home directory
and current directory.

This program use a modified version of Alessandro Guffanti (guffanti@tigem.it)
PaintBlast package drawimage function, in order to display a graphical
alignment summary; this function has been rewrited and integrated in source
code for easier program installation and use. The PaintBlast original package
is available at <URL:http://hercules.tigem.it/Biomodules/PaintBlast.pm>.
It needs the perl GD.pm package too (interface to Thomas Boutell's gd library)
for image support (v1.20 or more for Png format, Gif otherwise).

This program has been already tested with:
- NCBI Blast 1.4.7 up to 2.0.12
- PSI Blast up to 2.0.12
- Washington University Blast up to 2.0a19
- GCG 9.1 blast.

Any comments/suggestions should be adressed to:
Nicolas Joly (njoly@pasteur.fr).
