Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Formulations and hardness of multiple sorting by reversals
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
A Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
SIAM Journal on Computing
A Very Elementary Presentation of the Hannenhalli-Pevzner Theory
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
Edit Distances for Genome Comparisons Based on Non-Local Operations
CPM '92 Proceedings of the Third Annual Symposium on Combinatorial Pattern Matching
Journal of Computer and System Sciences
On the similarity of sets of permutations and its applications to genome comparison
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Using PQ trees for comparative genomics
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Hi-index | 0.00 |
Various international efforts are underway to catalog the genomic similarities and variations in the human population. Some key discoveries such as inversions and transpositions within the members of the species have also been made over the years. The task of constructing a phylogeny tree of the members of the same species, given this knowledge and data, is an important problem. In this context, a key observation is that the “distance” between two members, or member and ancestor, within the species is small. In this paper, we pose the tree reconstruction problem exploiting some of these peculiarities. The central idea of the paper is based on the notion of minimal consensus PQ tree T of sequences introduced in [29]. We use a modified PQ structure (termed oPQ) and show that both the number and size of each T is $\mathcal{O}(1)$. We further show that the tree reconstruction problem is statistically well-defined (Theorem [7]) and give a simple scheme to construct the phylogeny tree and the common ancestors. Our preliminary experiments with simulated data look very promising.