Who is Who in Phylogenetic Networks

Publications of Derek Ruths     Order by:   Type | Year

Associated keywords

coalescent counting explicit-network from-rooted-trees from-species-tree heuristic lateral-gene-transfer phylogenetic-network phylogeny polynomial Program-LatTrans Program-PhyloNet reconstruction software

Article (Journal)

1 Cuong Than, Derek Ruths and Luay Nakhleh. PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships. In BMCB, Vol. 9(322), 2008. Keywords: Program PhyloNet, software. Note: http://dx.doi.org/10.1186/1471-2105-9-322.         Toggle abstract "Background: Phylogenies, i.e., the evolutionary histories of groups of taxa, play a major role in representing the interrelationships among biological entities. Many software tools for reconstructing and evaluating such phylogenies have been proposed, almost all of which assume the underlying evolutionary history to be a tree. While trees give a satisfactory first-order approximation for many families of organisms, other families exhibit evolutionary mechanisms that cannot be represented by trees. Processes such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred to as reticulate evolutionary events, result in networks, rather than trees, of relationships. Various software tools have been recently developed to analyze reticulate evolutionary relationships, which include SplitsTree4, LatTrans, EEEP, HorizStory, and T-REX. Results: In this paper, we report on the PhyloNet software package, which is a suite of tools for analyzing reticulate evolutionary relationships, or evolutionary networks, which are rooted, directed, acyclic graphs, leaf-labeled by a set of taxa. These tools can be classified into four categories: (1) evolutionary network representation: reading/writing evolutionary networks in a newly devised compact form; (2) evolutionary network characterization: analyzing evolutionary networks in terms of three basic building blocks - trees, clusters, and tripartitions; (3) evolutionary network comparison: comparing two evolutionary networks in terms of topological dissimilarities, as well as fitness to sequence evolution under a maximum parsimony criterion; and (4) evolutionary network reconstruction: reconstructing an evolutionary network from a species tree and a set of gene trees. Conclusion: The software package, PhyloNet, offers an array of utilities to allow for efficient and accurate analysis of evolutionary networks. The software package will help significantly in analyzing large data sets, as well as in studying the performance of evolutionary network reconstruction methods. Further, the software package supports the proposed eNewick format for compact representation of evolutionary networks, a feature that allows for efficient interoperability of evolutionary network software tools. Currently, all utilities in PhyloNet are invoked on the command line. © 2008 Than et al; licensee BioMed Central Ltd." 2 Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. In JCB, Vol. 14(4):517-535, 2007. Keywords: counting, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet. Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-jcb.pdf.         3 Derek Ruths and Luay Nakhleh. Recombination and phylogeny: effects and detection. In IJBRA, Pages 202-212, 2005. Note: http://www.cs.rice.edu/~nakhleh/Papers/IJBRA05.pdf.

InProceedings

4 Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. In Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'06), Vol. 4205:215-229 of LNCS, springer, 2006. Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet. Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-final.pdf.         5 Luay Nakhleh, Derek Ruths and Li-San Wang. RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. In COCOON05, Vol. 3595:84-93 of LNCS, springer, 2005. Keywords: from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program PhyloNet. Note: http://www.cs.rice.edu/~nakhleh/Papers/COCOON05.pdf.

InBook

6 Luay Nakhleh, Derek Ruths and Hideki Innan. Gene Trees, Species Trees, and Species Networks. In R. Guerra, D. B. Allison and D. Goldstein editors, Meta-analysis and Combining Information in Genetics and Genomics, 2009. Keywords: coalescent, explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction. Note: http://www.cs.rice.edu/~nakhleh/Papers/GuerraGoldsteinBookChapter.pdf.

MastersThesis

7 Derek Ruths. Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer. Master's thesis, Rice University, U.S.A., 2005. Keywords: explicit network, from rooted trees, from species tree, heuristic, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://hdl.handle.net/1911/17912.