Software accompaniment to
Song, Y.S., Ding, Z., Gusfield, D., Langley, C.H., and Wu, Y.
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations,
Proceedings of RECOMB 2006, pp. 231-245.
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 HapBound-GC)
Example data sets
Example Ancestral Recombination Graph (ARG)
An ARG (for simulated data set 1) produced by SHRUB-GC using max tract length t=100.
Green vertices correspond to gene-coversions and blue vertices correspond to crossovers.
Vertex label [i,j] below a gene-conversion vertex denotes a closed interval contained in the conversion tract
Edge label "F": Flanking region
Edge label "T": Conversion Tract
Vertex label (i,j) below a crossover vertex denotes an open interval containing the crossover breakpoint.
Edge label "P": Prefix
Edge label "S": Suffix
Numerical labels on edges correspond to site mutations.
Recommended software for viewing the ARGs generated by SHRUB
GIF files needed for graphics