Who is Who in Phylogenetic Networks

Publication no #2260   Type :   Html | Bib | Both

Created: 2012-09-30 23:27:24     Modified: 2016-06-30 01:16:23

2260 Katharina Huber, Vincent Moulton, Andreas Spillner, Sabine Storandt and Radoslaw Suchecki. Computing a consensus of multilabeled trees. In ALENEX12, Pages 84-92, 2012. Keywords: duplication, explicit network, exponential algorithm, phylogenetic network, phylogeny. Note: http://siam.omnibooksonline.com/2012ALENEX/data/papers/020.pdf.         Toggle abstract In this paper we consider two challenging problems that arise in the context of computing a consensus of a collection of multilabeled trees, namely (1) selecting a compatible collection of clusters on a multiset from an ordered list of such clusters and (2) optimally refining high degree vertices in a multilabeled tree. Forming such a consensus is part of an approach to reconstruct the evolutionary history of a set of species for which events such as genome duplication and hybridization have occurred in the past. We present exact algorithms for solving (1) and (2) that have an exponential run-time in the worst case. To give some impression of their performance in practice, we apply them to simulated input and to a real biological data set highlighting the impact of several structural properties of the input on the performance. @InProceedings{HMSSS2012,       AUTHOR = {Huber, Katharina and Moulton, Vincent and Spillner, Andreas and Storandt, Sabine and Suchecki, Radoslaw},       TITLE = {Computing a consensus of multilabeled trees},       YEAR = {2012},       BOOKTITLE = {ALENEX12},       PAGES = {84-92},       URL = {http://dx.doi.org/10.1137/1.9781611972924.9},       NOTE = {http://siam.omnibooksonline.com/2012ALENEX/data/papers/020.pdf},       KEYWORDS = {duplication, explicit network, exponential algorithm, phylogenetic network, phylogeny} }