TY - GEN

T1 - Reconstructing an ultrametric galled phylogenetic network from a distance matrix

AU - Chan, Ho Leung

AU - Jansson, Jesper Andreas

AU - Lam, Tak Wah

AU - Yiu, Siu Ming

PY - 2005/10/24

Y1 - 2005/10/24

N2 - Given a distance matrix M that specifies the pairwise evolutionary distances between n species, the phylogenetic tree reconstruction problem asks for an edge-weighted phylogenetic tree that satisfies M, if one exists. We study some extensions of this problem to rooted phylogenetic networks. Our main result is an O(n2 log n)-time algorithm for determining whether there is an ultrametric galled network that satisfies M, and if so, constructing one. In fact, if such an ultrametric galled network exists, our algorithm is guaranteed to construct one containing the minimum possible number of nodes with more than one parent (hybrid nodes). We also prove that finding a largest possible submatrix M′ of M such that there exists an ultrametric galled network that satisfies M′ is NP-hard. Furthermore, we show that given an incomplete distance matrix (i.e., where some matrix entries are missing), it is also NP-hard to determine whether there exists an ultrametric galled network which satisfies it.

AB - Given a distance matrix M that specifies the pairwise evolutionary distances between n species, the phylogenetic tree reconstruction problem asks for an edge-weighted phylogenetic tree that satisfies M, if one exists. We study some extensions of this problem to rooted phylogenetic networks. Our main result is an O(n2 log n)-time algorithm for determining whether there is an ultrametric galled network that satisfies M, and if so, constructing one. In fact, if such an ultrametric galled network exists, our algorithm is guaranteed to construct one containing the minimum possible number of nodes with more than one parent (hybrid nodes). We also prove that finding a largest possible submatrix M′ of M such that there exists an ultrametric galled network that satisfies M′ is NP-hard. Furthermore, we show that given an incomplete distance matrix (i.e., where some matrix entries are missing), it is also NP-hard to determine whether there exists an ultrametric galled network which satisfies it.

UR - http://www.scopus.com/inward/record.url?scp=26844460384&partnerID=8YFLogxK

M3 - Conference article published in proceeding or book

T3 - Lecture Notes in Computer Science

SP - 224

EP - 235

BT - Mathematical Foundations of Computer Science 2005: 30th International Symposium, MFCS 2005, Gdansk, Poland, August 29-September 2, 2005. Proceedings

A2 - Jedrzejowicz, Joanna

A2 - Szepietowski, Andrzej

T2 - 30th International Symposium on Mathematical Foundations of Computer Science 2005, MFCS 2005

Y2 - 29 August 2005 through 2 September 2005

ER -