Comparison of Galled Trees

Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial-time algorithms for their reconstruction. In this paper, we establish to which extent several distance measures for the comparison of evolutionary networks are metrics for galled trees, and hence, when they can be safely used to evaluate galled tree reconstruction methods.

[1]  Gabriel Cardona,et al.  Path lengths in tree-child time consistent hybridization networks , 2008, Inf. Sci..

[2]  Philippe Gambette,et al.  On encodings of phylogenetic networks of bounded level , 2009, Journal of mathematical biology.

[3]  Tandy J. Warnow,et al.  Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods , 2002, Pacific Symposium on Biocomputing.

[4]  Gabriel Cardona,et al.  Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric , 2009, IEEE ACM Trans. Comput. Biol. Bioinform..

[5]  Gabriel Cardona,et al.  Tripartitions do not always discriminate phylogenetic networks , 2008, Mathematical biosciences.

[6]  Dan Gusfield,et al.  Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination , 2004, J. Bioinform. Comput. Biol..

[7]  G. Valiente,et al.  Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric , 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[8]  Kaizhong Zhang,et al.  Perfect phylogenetic networks with recombination , 2001, J. Comput. Biol..

[9]  Gabriel Cardona,et al.  On Nakhleh's Metric for Reduced Phylogenetic Networks , 2009, TCBB.

[10]  Gabriel Cardona,et al.  Comparison of Tree-Child Phylogenetic Networks , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[11]  Wing-Kin Sung,et al.  The Maximum Agreement of Two Nested Phylogenetic Networks , 2004, ISAAC.

[12]  Yun S. Song,et al.  A Decomposition Theory for Phylogenetic Networks and Incompatible Characters , 2007, J. Comput. Biol..

[13]  L. Nakhleh,et al.  A Metric on the Space of Reduced Phylogenetic Networks , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[14]  Daniel H. Huson,et al.  Beyond Galled Trees - Decomposition and Computation of Galled Networks , 2007, RECOMB.

[15]  L. Stougie,et al.  Constructing Level-2 Phylogenetic Networks from Triplets , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[16]  Siu-Ming Yiu,et al.  Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix , 2005, MFCS.

[17]  D. Posada,et al.  Characterization of Reticulate Networks Based on the Coalescent with Recombination , 2008, Molecular biology and evolution.

[18]  Steven Skiena,et al.  Lowest common ancestors in trees and directed acyclic graphs , 2005, J. Algorithms.

[19]  Tandy J. Warnow,et al.  Phylogenetic networks: modeling, reconstructibility, and accuracy , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[20]  Joan Oliver Araujo,et al.  The University of the Balearic Islands , 1993 .

[21]  G. Valiente,et al.  Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics , 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[22]  Wing-Kin Sung,et al.  Algorithms for combining rooted triplets into a galled phylogenetic network , 2005, SODA '05.

[23]  Charles Semple,et al.  A Framework for Representing Reticulate Evolution , 2005 .

[24]  Wing-Kin Sung,et al.  Inferring a Level-1 Phylogenetic Network from a Dense Set of Rooted Triplets , 2004, COCOON.

[25]  J. Farris.  On Comparing the Shapes of Taxonomic Trees , 1973 .

[26]  Charles Semple,et al.  Hybrids in real time. , 2006, Systematic biology.

[27]  Gabriel Cardona,et al.  Nodal distances for rooted phylogenetic trees , 2008, Journal of mathematical biology.

[28]  Charles Semple,et al.  Computing the minimum number of hybridization events for a consistent evolutionary history , 2007, Discret. Appl. Math..

[29]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[30]  Tandy J. Warnow,et al.  Reconstructing reticulate evolution in species: theory and practice , 2004, RECOMB.

[31]  D. Huson,et al.  Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.

[32]  Dan Gusfield,et al.  Efficient reconstruction of phylogenetic networks with constrained recombination , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[33]  Luay Nakhleh,et al.  Phylogenetic networks , 2004 .

[34]  Bin Ma,et al.  Fixed topology alignment with recombination , 1998, Discrete Applied Mathematics.

[35]  Francesc Rosselló,et al.  All that Glisters is not Galled , 2009, Mathematical biosciences.

[36]  A. Dress,et al.  Split decomposition: a new and useful approach to phylogenetic analysis of distance data. , 1992, Molecular phylogenetics and evolution.

[37]  M. Miyamoto,et al.  Phylogenetic Analysis of DNA Sequences , 1991 .

[38]  W. T. Williams,et al.  ON THE COMPARISON OF TWO CLASSIFICATIONS OF THE SAME SET OF ELEMENTS , 1971 .

[39]  Gabriel Cardona,et al.  A distance metric for a class of tree-sibling phylogenetic networks , 2008, Bioinform..

[40]  Dan Gusfield,et al.  The Fine Structure of Galls in Phylogenetic Networks , 2004, INFORMS J. Comput..

[41]  Kunihiko Sadakane,et al.  Computing the Maximum Agreement of Phylogenetic Networks , 2004, CATS.