On the complexity of comparing evolutionary trees
Discrete Applied Mathematics - Special volume on computational molecular biology
Efficient algorithms for lateral gene transfer problems
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
TreeJuxtaposer: scalable tree comparison using Focus+Context with guaranteed visibility
ACM SIGGRAPH 2003 Papers
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computing the minimum number of hybridization events for a consistent evolutionary history
Discrete Applied Mathematics
Efficient haplotype inference with boolean satisfiability
AAAI'06 Proceedings of the 21st national conference on Artificial intelligence - Volume 1
SATzilla: portfolio-based algorithm selection for SAT
Journal of Artificial Intelligence Research
Combining adaptive noise and look-ahead in local search for SAT
SAT'07 Proceedings of the 10th international conference on Theory and applications of satisfiability testing
UBCSAT: an implementation and experimentation environment for SLS algorithms for SAT and MAX-SAT
SAT'04 Proceedings of the 7th international conference on Theory and Applications of Satisfiability Testing
RIATA-HGT: a fast and accurate heuristic for reconstructing horizontal gene transfer
COCOON'05 Proceedings of the 11th annual international conference on Computing and Combinatorics
Extending clause learning of SAT solvers with Boolean Gröbner bases
CASC'10 Proceedings of the 12th international conference on Computer algebra in scientific computing
Empirical study of the anatomy of modern sat solvers
SAT'11 Proceedings of the 14th international conference on Theory and application of satisfiability testing
Fast FPT algorithms for computing rooted agreement forests: theory and experiments
SEA'10 Proceedings of the 9th international conference on Experimental Algorithms
Verifying refutations with extended resolution
CADE'13 Proceedings of the 24th international conference on Automated Deduction
Automated reencoding of boolean formulas
HVC'12 Proceedings of the 8th international conference on Hardware and Software: verification and testing
Hi-index | 0.00 |
We develop techniques to calculate important measures in evolutionary biology by encoding to CNF formulas and using powerful SAT solvers. Comparing evolutionary trees is a necessary step in tree reconstruction algorithms, locating recombination and lateral gene transfer, and in analyzing and visualizing sets of trees. We focus on two popular comparison measures for trees: the hybridization number and the rooted subtree-prune-and-regraft (rSPR) distance. Both have recently been shown to be NP-hard, and efficient algorithms are needed to compute and approximate these measures. We encode these as a Boolean formula such that two trees have hybridization number k (or rSPR distance k ) if and only if the corresponding formula is satisfiable. We use state-of-the-art SAT solvers to determine if the formula encoding the measure has a satisfying assignment. Our encoding also provides a rich source of real-world SAT instances, and we include a comparison of several recent solvers (minisat, adaptg2wsat, novelty+p, Walksat, March KS and SATzilla).