Detecting Crossover Recombination
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HapBound and SHRUB
[ Link ]
Software accompaniment to
"Song, Y.S., Wu, Y. and Gusfield, D.
Efficient computation of close lower and upper bounds on the minimum number of
recombinations in biological sequence evolution,
Proceedings of ISMB 2005.
Bioinformatics, 21, Suppl.1, (2005) i413-i422."
HapBound and SHRUB respectively compute lower and upper bounds on the minimum number of crossover recombinations.
SHRUB constructs an ancestral recombination graph for the input data.
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Beagle
[ Link ]
Software accompaniment to
"Lyngsø, R., Song, Y.S., and Hein, J.
Minimum Recombination Histories by Branch and Bound.
Proceedings of WABI 2005,
Lecture Notes in Computer Science, 3692, pp. 239-250."
Beagle computes the minimum number of crossover recombinations. It also produces an ancestral recombination graph.
Detecting Crossover and Gene-Conversion Recombinations
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HapBound-GC and SHRUB-GC
[ Link ]
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.
Lecture Notes in Computer Science 3909, (2006) 231-245."
HapBound-GC and SHRUB-GC respectively compute lower and upper bounds on the minimum combined number of crossover and gene-conversion recombinations.
SHRUB-GC constructs a graphical representation of evolutionary history involving coalescent, mutation, crossover and gene-conversion events.