SIBsim4 project


The SIBsim4 project is based on sim4, which is a program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns. Sim4 was written by Liliana Florea while working in Webb Miller's lab at the Pennsylvania State University. Here is the paper describing sim4, and here is the original source code.


SIBsim4 is a fairly extensive rewrite of the original code with the following goals:


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.

The SIBsim4 project is kindly hosted by SourceForge here.

There is a manpage available, as well as a list of changes wrt the original sim4.

The current version of SIBsim4 is 0.17. It is available from the sourceforge page. The list of changes from the previous versions is available in the changes page. This code has now seen quite a bit of testing and should be stable. Bug reports (and enough data to reproduce them) welcome. Logo

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