Estimating Recombination Rates
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LDhelmet
[ Link ]
Software accompaniment to
"Chan, A.H., Jenkins, P.A., and Song, Y.S.
Genome-wide fine-scale recombination rate variation in Drosophila melanogaster.
PLoS Genetics, vol. 8 no. 12 (2012) e1003090."
LDhelmet is a statistical method based on reversible jump MCMC and composite likelihood. It samples piecewise constant recombination maps from a posterior distribution.
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COB
[ Link ]
Software accompaniment to
"Lyngsų, R., Song, Y.S., and Hein, J.
Accurate computation of likelihoods in the coalescent with recombination via parsimony.
Proc. 12th Annual Intl. Conf. on Research in Computational Molecular Biology (RECOMB 2008),
Lecture Notes in Computer Science 4955, pages 463--477."
COB is a parsimony-based method of computing likelihoods accurately under the coalescent with
recombination.
Gene Conversion
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Overpaint
[ Link ]
Software accompaniment to
"Yin, J. Jordan, M. I., and Song, Y. S..
Joint estimation of gene conversion rates
and mean conversion tract lengths from population SNP data,
Proceedings of ISMB 2009, Bioinformatics, 25 (2009) i231-i239."
Short-Read Error Correction
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ECHO
[ Link ]
Software accompaniment to
"Kao, W.-C., Chan, A. H., and Song, Y. S.
ECHO: A reference-free short-read error correction algorithm,
Genome Research,
21 (2011) 1181-1192"
Basecaller for the Illumina Platform
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(naive)BayesCall
[ Link ]
Software accompaniment to
"Kao, W.C., Stevens, K. and Song, Y.S.
BayesCall: A model-based basecalling algorithm for high-throughput short-read sequencing.
Genome Research,
19 (2009) 1884-1895."
Kao, W.C. and Song, Y.S.
naiveBayesCall: An efficient model-based base-calling algorithm for high-throughput sequencing.
Proc. 14th Annual Intl. Conf. on Research in Computational Molecular Biology
(RECOMB 2010),
Lecture Notes in Computer Science 6044, pages 233--247, 2010.
(A new base-calling algorithm that builds on our previous method BayesCall to achieve scalability.)
Two-Locus Asymptotic Sampling Formula
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ASF
[ Link ]
Software accompaniment to
"Jenkins, P.A. and Song, Y.S.
Closed-form two-locus sampling distributions: accuracy and universality
Genetics, 183 (2009) 1087-1103."
Multi-locus Match Probability
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Wright_Fisher_MP and
Moran_MP
[ Link ]
Software accompaniment to
"Bhaskar, A. and Song, Y.S.
Multi-locus match probability in a finite population: A fundamental difference between the Moran and Wright-Fisher models.
Proceedings of ISMB 2009, Bioinformatics, 25 (2009) i187-i195."
Whole-Genome Association Mapping
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BLOSSOC
[ Link ]
Software accompaniment to
"Ding, Z., Mailund, T., and Song, Y.S.
Efficient whole-genome association mapping using local phylogenies for
unphased genotype data.
Bioinformatics, 24 (2008) 2215-2221."
This program combines a recently found linear-time algorithm
for phasing genotypes on trees with a
tree-based method for association mapping. From unphased
genotype data, our algorithm builds local phylogenies along the
genome, and scores each tree according to the clustering of
cases and controls.
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.