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. SIBsim4 is an extensive rewrite of the sim4 program to improve execution speed and provide more informative output.
Release Notes: This release introduces a new command line switch, -S, which allows one to better fine tune how insertions/deletions are evaluated around potential splice junctions. A few problems, where spurious very small exons or large gaps in exons were incorrectly reported, have been fixed. The code was cleaned up to silence new warnings from the current GCC releases.
Release Notes: This release introduces a chimera detection feature.
Release Notes: This release fixes excessive run-time in some cases of partially repeated sequences. All users are encouraged to update.
Release Notes: This release adds a -s option to better control how potential duplicated genes are detected, instead of abusing the -f option.
Release Notes: This version introduces two new options, -c and -f, which provide full control over how results are filtered. This allows better detection of duplicated genes, where duplicates are incomplete or not well preserved.