HapBound-GC and SHRUB-GC

HapBound-GC and SHRUB-GC

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.

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 HapBound-GC)

Lower bound

HapBound-GC (executable file compiled under Redhat Linux Enterprise)
HapBound-GC-mac (executable file compiled under Mac OS X)
README file for HapBound-GC
GNU copyright information

Upper bound

SHRUB-GC (executable file compiled under Redhat Linux Enterprise)
SHRUB-GC-mac (executable file compiled under Mac OS X)
README file for SHRUB-GC

Example data sets

Simulated data set 1 (generated using Hudson's MS with n=20, s=30, rho=5, f=5)
Simulated data set 2 (generated using Hudson's MS with n=20, s=30, rho=5, f=2.5)

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

VGJ, Visualizing Graphs with Java

GIF files needed for graphics

red-ball.gif (for leaves)
blue-ball.gif (for crossover vertices)
green-ball.gif (for gene-conversion vertices)
white-ball.gif (for coalescent vertices)