Who is Who in Phylogenetic Networks

Publication no #2142   Type :   Html | Bib | Both

Created: 2011-10-18 00:28:48     Modified: 2018-08-17 08:19:39

2142 Katharina Huber and Vincent Moulton. Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets. In ALG, Vol. 66(3):714-738, 2013. Keywords: explicit network, from subnetworks, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://arxiv.org/abs/1110.0728.         Toggle abstract "Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from biological data using triplets, i.e. binary phylogenetic trees on 3-element subsets of a given set of species. However, a fundamental problem with this approach is that the triplets displayed by a phylogenetic network do not necessarily uniquely determine or encode the network. Here we propose an alternative approach to encoding and constructing phylogenetic networks, which uses phylogenetic networks on 3-element subsets of a set, or trinets, rather than triplets. More specifically, we show that for a special, well-studied type of phylogenetic network called a 1-nested network, the trinets displayed by a 1-nested network always encode the network. We also present an efficient algorithm for deciding whether a dense set of trinets (i.e. one that contains a trinet on every 3-element subset of a set) can be displayed by a 1-nested network or not and, if so, constructs that network. In addition, we discuss some potential new directions that this new approach opens up for constructing and comparing phylogenetic networks. © 2012 Springer Science+Business Media, LLC." @Article{HuberMoulton2013,       AUTHOR = {Huber, Katharina and Moulton, Vincent},       TITLE = {Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets},       YEAR = {2013},       JOURNAL = {ALG},       VOLUME = {66},       NUMBER = {3},       PAGES = {714-738},       URL = {http://dx.doi.org/10.1007/s00453-012-9659-x},       NOTE = {http://arxiv.org/abs/1110.0728},       KEYWORDS = {explicit network, from subnetworks, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness} }