Metabolic Flux Estimation-A Self-Adaptive Evolutionary Algorithm with Singular Value Decomposition
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
ReCombinatorics: Combinatorial Algorithms for Studying the History of Recombination in Populations
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
COCOA 2008 Proceedings of the 2nd international conference on Combinatorial Optimization and Applications
Information Processing Letters
Counting Faces in Split Networks
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Accurate computation of likelihoods in the coalescent with recombination via parsimony
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Genome-wide compatible SNP intervals and their properties
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
New Methods for Inference of Local Tree Topologies with Recombinant SNP Sequences in Populations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Large neighbourhood search algorithms for the founder sequence reconstruction problem
Computers and Operations Research
An evolutionary approach to the inference of phylogenetic networks
PPSN'06 Proceedings of the 9th international conference on Parallel Problem Solving from Nature
Efficient and practical algorithms for deducing the history of recombination in populations
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Improved algorithms for inferring the minimum mosaic of a set of recombinants
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
A new recombination lower bound and the minimum perfect phylogenetic forest problem
COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics
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Motivation: We are interested in studying the evolution of DNA single nucleotide polymorphism sequences which have undergone (meiotic) recombination. For a given set of sequences, computing the minimum number of recombinations needed to explain the sequences (with one mutation per site) is a standard question of interest, but it has been shown to be NP-hard, and previous algorithms that compute it exactly work either only on very small datasets or on problems with special structure. Results: In this paper, we present efficient, practical methods for computing both upper and lower bounds on the minimum number of needed recombinations, and for constructing evolutionary histories that explain the input sequences. We study in detail the efficiency and accuracy of these algorithms on both simulated and real data sets. The algorithms produce very close upper and lower bounds, which match exactly in a surprisingly wide range of data. Thus, with the use of new, very effective lower bounding methods and an efficient algorithm for computing upper bounds, this approach allows the efficient, exact computation of the minimum number of needed recombinations, with high frequency in a large range of data. When upper and lower bounds match, evolutionary histories found by our algorithm correspond to the most parsimonious histories. Availability: HapBound and SHRUB, programs implementing the new algorithms discussed in this paper, are available at http://wwwcsif.cs.ucdavis.edu/~gusfield/lu.html Contact: yssong@cs.ucdavis.edu