Who is Who in Phylogenetic Networks

Publications related to 'Program Marlon' : MARLON (Minimum Amount of Reticulation Level One Network) is a program which reconstructs a level-1 phylogenetic network (i.e. galled tree), with the minimum number of reticulation nodes, from a set of triplets. Available at http://skelk.sdf-eu.org/marlon.html.   Order by:   Type | Year

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Associated keywords

evaluation explicit-network exponential-algorithm FPT from-triplets galled-tree level-k-phylogenetic-network minimum-number mu-distance phylogenetic-network phylogeny polynomial Program-Level2 Program-Marlon Program-Simplistic Program-T-REX reconstruction

Article (Journal)

1 Leo van Iersel and Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ALG, Vol. 60(2):207-235, 2011. Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic. Note: http://dx.doi.org/10.1007/s00453-009-9333-0.         Toggle abstract "A phylogenetic network is a directed acyclic graph that visualizes an evolutionary history containing so-called reticulations such as recombinations, hybridizations or lateral gene transfers. Here we consider the construction of a simplest possible phylogenetic network consistent with an input set T, where T contains at least one phylogenetic tree on three leaves (a triplet) for each combination of three taxa. To quantify the complexity of a network we consider both the total number of reticulations and the number of reticulations per biconnected component, called the level of the network. We give polynomial-time algorithms for constructing a level-1 respectively a level-2 network that contains a minimum number of reticulations and is consistent with T (if such a network exists). In addition, we show that if T is precisely equal to the set of triplets consistent with some network, then we can construct such a network with smallest possible level in time O(|T| k+1), if k is a fixed upper bound on the level of the network. © 2009 The Author(s)."

InProceedings

2 Leo van Iersel and Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ISAAC08, Vol. 5369:472-483 of LNCS, springer, 2008. Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic. Note: http://arxiv.org/abs/0805.1859.

PhdThesis

3 Leo van Iersel. Algorithms, Haplotypes and Phylogenetic Networks. PhD thesis, Eindhoven University of Technology, The Netherlands, 2009. Keywords: evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction. Note: http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf.