TY - GEN

T1 - Inferring a level-1 phylogenetic network from a dense set of rooted triplets

AU - Jansson, Jesper Andreas

AU - Sung, Wing Kin

PY - 2004

Y1 - 2004

N2 - Given a set T of rooted triplets with leaf set L, we consider the problem of determining whether there exists a phylogenetic network consistent with T, and if so, constructing one. If no restrictions are placed on the hybrid nodes in the solution, the problem is trivially solved in polynomial time by a simple sorting network-based construction. For the more interesting (and biologically more motivated) case where the solution is required to be a level-1 phylogenetic network, we present an algorithm solving the problem in O(n6) time when T is dense (i.e., contains at least one rooted triplet for each cardinality three subset of L), where n = |L|. Note that the size of the input is Θ(n3) if T is dense. We also give an O(n5)-time algorithm for finding the set of all phylogenetic networks having a single hybrid node attached to exactly one leaf (and having no other hybrid nodes) that are consistent with a given dense set of rooted triplets.

AB - Given a set T of rooted triplets with leaf set L, we consider the problem of determining whether there exists a phylogenetic network consistent with T, and if so, constructing one. If no restrictions are placed on the hybrid nodes in the solution, the problem is trivially solved in polynomial time by a simple sorting network-based construction. For the more interesting (and biologically more motivated) case where the solution is required to be a level-1 phylogenetic network, we present an algorithm solving the problem in O(n6) time when T is dense (i.e., contains at least one rooted triplet for each cardinality three subset of L), where n = |L|. Note that the size of the input is Θ(n3) if T is dense. We also give an O(n5)-time algorithm for finding the set of all phylogenetic networks having a single hybrid node attached to exactly one leaf (and having no other hybrid nodes) that are consistent with a given dense set of rooted triplets.

UR - http://www.scopus.com/inward/record.url?scp=35048857956&partnerID=8YFLogxK

M3 - Conference article published in proceeding or book

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 462

EP - 471

BT - Computing and Combinatorics: 10th Annual International Conference, COCOON 2004, Jeju Island, Korea, August 2004 Proceedings

A2 - Chwa, Kyung-Yong

A2 - Munro, J. Ian

T2 - 10th Annual International Computing and Combinatorics Conference, COCOON 2004

Y2 - 17 August 2004 through 20 August 2004

ER -