| This package (SIBsim4) implements a variation of the Sim4 algorithm, |
| as described below, originally written by Liliana Florea and Scott |
| Schwartz. The modifications were written by Claudio Lottaz and |
| Christian Iseli, while working for the Swiss Institute of |
| Bioinformatics and the Ludwig Institute for Cancer Research. |
| |
| The modifications are Copyright (c) Swiss Institute of Bioinformatics, |
| and Ludwig Institute for Cancer Research (LICR), 2001-2004. For the |
| purposes of this copyright, the Swiss Institute of Bioinformatics acts |
| on behalf of its partner, LICR. |
| |
| The resulting, modified, package is licensed 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. |
| |
| Below is the original copyright notice. |
| |
| ----------------------------------------------------------------------- |
| |
| This package implements the Sim4 algorithm for aligning expressed DNA |
| with genomic sequences, described in the paper: |
| |
| L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998) |
| "A computer program for aligning a cDNA sequence with a genomic DNA sequence." |
| Genome Research 8, 967-974. |
| |
| |
| Portions copyright by: |
| |
| Copyright (C) 1998-2001 Liliana Florea |
| Copyright (C) 1998-2001 Scott Schwartz |
| |
| 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. |
| |
| 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
| |
| # The following files were written by Liliana Florea: |
| |
| Xtend1.c |
| Xtend1.h |
| align.c |
| align.h |
| sim4.h |
| sim4.init.c |
| sim4b1.c |
| sim4b1.h |
| splice.c |
| splice.h |
| |
| # The following files were written by Scott Schwartz: |
| |
| args.c |
| args.h |
| charvec.c |
| charvec.h |
| discrim.c |
| discrim.h |
| dna.c |
| dna.h |
| encoding.c |
| encoding.h |
| libc.h |
| misc.c |
| misc.h |
| prnt.c |
| prnt.h |
| psublast.h |
| seq.c |
| seq.h |
| seq_read.c |
| types.h |