SIBsim4 0.15

SIBsim4 project is based on sim4, which is a program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns.
SIBsim4 is an extensive rewrite of the sim4 program to improve execution speed and provide more informative output.
The name was chosen to denote the fact the SIBsim4 is a derivative work from sim4. SIB stands for the Swiss Institute of Bioinformatics. Some code modifications were written by Claudio Lottaz, while working at SIB.
SIBsim4 is currently developed and maintained by Christian Iseli, from the Ludwig Institute for Cancer Research LICR, Information Technology Office in Lausanne. LICR is a SIB partner.
Main features:
- speed improvement
- allow large, chromosome scale, DNA sequences to be used
- provide more detailed output about splice types
- provide more detailed output about polyA sites
- misc code cleanups and fixes
Enhancements:
- This release add a -s option to control how potential duplicated genes aer detected, instead of abusing the -f option.