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AltSplicingToolkit contains a set of tools to compute information
regarding alternative splicing. At the moment, this toolkit contains
one binary program called:

altSpliceFinder

altSpliceFinder is an extensible and generic tool to compute recurrent 
alternative splicing patterns from a set of transcripts variants. 
It takes a GFF3 file as an input containing a list of transcript
structures in terms of exons and generates a GFF3 file containing the
resulting set of alternative splicing events.

Currently altSpliceFinder is able to find the following types of 
splicing events:
	- Cassette exons (skipped exons)
	- Intron retention
	- Mutually exclusive exons
	- Alternative 3' sites
	- Alternative 5' sites
	- Intron isoform
	- Exon isoform
	- Alternative first exon
	- Alternative last exon
	- Alternative initiation
	- Alternative termination

This program is also able to list constitutive exons from a set of
splicing variants.

The file INSTALL should be distributed with packages that use
Autoconf-generated configure scripts and Makefiles that conform to the
GNU coding standards.  The package's README can just give an overview
of the package, where to report bugs, and a pointer to INSTALL for
instructions on compilation and installation.  This removes the need
to maintain many similar sets of installation instructions.

Be sure to read BUGS (especially if this version is not an official
release) and INSTALL.

Licensing

AltSplicingToolkit is released under the Ensembl Licence.

For more licensing information, see
<http://www.ensembl.org/info/about/code_licence.html>.


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 Copyright (c) 1999-2011 The European Bioinformatics Institute and 
 Genome Research Limited, and others.  All rights reserved. 

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
Ensembl License for more details.

You should have received a copy of the Ensembl License
along with this program.  If not, see 
<http://www.ensembl.org/info/about/code_licence.html>.
