HTML4BLAST

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.
  -n        ... No databases links.
  -o <file> ... Set output to <file> [blast.html].
  -q        ... Generate query based image names.
  -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 Retrieval 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
respectively 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
rewritten 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 2.1.3
- NCBI PSI Blast up to 2.1.3
- Washington University Blast up to 2.0
- GCG 9.1 blast.

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