Who is Who in Phylogenetic Networks

Publications related to 'Program Hybroscale' : Available at a href https: drupal.bio.ifi.lmu.de en softwareservices hybroscale index.html https: drupal.bio.ifi.lmu.de en softwareservices hybroscale index.html a   Order by:   Type | Year

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agreement-forest explicit-network exponential-algorithm FPT from-rooted-trees minimum-number phylogenetic-network phylogeny polynomial Program-Dendroscope Program-Hybroscale Program-PIRN reconstruction software

2015

1 Benjamin Albrecht. Computing all hybridization networks for multiple binary phylogenetic input trees. In BMCB, Vol. 16(236):1-15, 2015. Keywords: agreement forest, explicit network, exponential algorithm, FPT, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, Program PIRN, reconstruction. Note: http://dx.doi.org/10.1186/s12859-015-0660-7.         2 Benjamin Albrecht. Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests. 2015. Keywords: agreement forest, explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software. Note: http://arxiv.org/abs/1512.05703.         3 Benjamin Albrecht. Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees. 2015. Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software. Note: http://arxiv.org/abs/1512.05656.

2014

4 Benjamin Albrecht. Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests. 2014. Keywords: agreement forest, from rooted trees, minimum number, phylogenetic network, phylogeny, polynomial, Program Hybroscale, reconstruction. Note: http://arxiv.org/abs/1408.3044.

2012

5 Celine Scornavacca, Simone Linz and Benjamin Albrecht. A first step towards computing all hybridization networks for two rooted binary phylogenetic trees. In JCB, Vol. 19:1227-1242, 2012. Keywords: agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction. Note: http://arxiv.org/abs/1109.3268.         Toggle abstract "Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard app1235roach to tackle this problem being combinatorial, the reconstructed network is rarely unique. From a biological point of view, it is therefore of importance to not only compute one network, but all possible networks. In this article, we make a first step toward approaching this goal by presenting the first algorithm-called allMAAFs-that calculates all maximum-acyclic-agreement forests for two rooted binary phylogenetic trees on the same set of taxa. © Copyright 2012, Mary Ann Liebert, Inc. 2012." 6 Benjamin Albrecht, Celine Scornavacca, Alberto Cenci and Daniel H. Huson. Fast computation of minimum hybridization networks. In BIO, Vol. 28(2):191-197, 2012. Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btr618.         Toggle abstract "Motivation: Hybridization events in evolution may lead to incongruent gene trees. One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events. Results: We describe how to compute a representative set of minimum hybridization networks for two given bifurcating input trees, using a parallel algorithm and provide a user-friendly implementation. A simulation study suggests that our program performs significantly better than existing software on biologically relevant data. Finally, we demonstrate the application of such methods in the context of the evolution of the Aegilops/Triticum genera. Availability and implementation: The algorithm is implemented in the program Dendroscope 3, which is freely available from www.dendroscope.org and runs on all three major operating systems. © The Author 2011. Published by Oxford University Press. All rights reserved."