RecBlock

Mosaic example
Software accompaniment to
Yufeng Wu and Dan Gusfield,  Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants, in Proceedings of Combinatorial Pattern Matching (CPM) 2007, pp. 150-161.

RecBlock is a program for finding the optimal mosaic pattern for recombinant population SNP sequences. Here is the basic idea. Suppose for some region of the genome, extant sequences are formed by a small number of founder sequences. Due to recombination, extant sequences are mosaic of founder sequences. The above figure shows an example, where there are 4 founders and 20 population sequences. See my paper for more details.

Note: Files can be downloaded using "Save Link/Target As..." After downloading the softwares, you may need to change file access permissions (e.g. chmod u+x RecBlock). Source code is available upon request .

Source code available upon request.