Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
STOC '95 Proceedings of the twenty-seventh annual ACM symposium on Theory of computing
Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Faster and simpler algorithm for sorting signed permutations by reversals
SODA '97 Proceedings of the eighth annual ACM-SIAM symposium on Discrete algorithms
Edit Distances for Genome Comparisons Based on Non-Local Operations
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
Efficient Bounds for Oriented Chromosome Inversion Distance
CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
CPM '96 Proceedings of the 7th Annual Symposium on Combinatorial Pattern Matching
Using PQ trees for comparative genomics
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
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When the same set of genes appear in different orders on the chromosomes, they form a permutation pattern. Permutation patterns have been used to identify potential haplogroups in mammalian data [8]. They also have been successfully used to detect phylogenetic relationships between computer viruses [9]. In this paper we explore the use of these patterns as a content similarity measure and use this in inferring phylogenies from genome rearrangement data in polynomial time. The method uses a function of the cardinality of the set of common maximal permutation patterns as a proxy for evolutionary “proximity” between genomes. We introduce Pi-logen, a phylogeny tool based on this method. We summarize results of feasibility study for this scheme on synthetic data by (1) content verification and (2) ancestor prediction. We also successfully infer phylogenies on series of synthetic data and on chloroplast gene order of Campanulaceae data.