Who is Who in Phylogenetic Networks

Publications of Year 2002

Article (Journal)

1 David Posada, Keith A. Crandall and Edward C. Holmes. Recombination in Evolutionary Genomics. In ARG, Vol. 36:75-97, 2002. Keywords: phylogenetic network, phylogeny, recombination, recombination detection, survey. Note: http://dx.doi.org/10.1146/annurev.genet.36.040202.111115.         Toggle abstract "Recombination can be a dominant force in shaping genomes and associated phenotypes. To better understand the impact of recombination on genomic evolution, we need to be able to identify recombination in aligned sequences. We review bioinformatic approaches for detecting recombination and measuring recombination rates. We also examine the impact of recombination on the reconstruction of evolutionary histories and the estimation of population genetic parameters. Finally, we review the role of recombination in the evolutionary history of bacteria, viruses, and human mitochondria. We conclude by highlighting a number of areas for future development of tools to help quantify the role of recombination in genomic evolution." 2 David Posada and Keith A. Crandall. The effect of recombination on the accuracy of phylogeny estimation. In JME, Pages 396-402, 2002. Note: http://darwin.uvigo.es/download/papers/17.recPhylo02.pdf.         3 Luay Nakhleh, Don Ringe and Tandy Warnow. Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages. In Language, Journal of the Linguistic Society of America, Vol. 81(2):382-420, 2002. Keywords: perfect, phylogenetic network, phylogeny. Note: http://www.cs.rice.edu/~nakhleh/Papers/81.2nakhleh.pdf.         4 Pierre Legendre and Vladimir Makarenkov. Reconstruction of biogeographic and evolutionary networks using reticulograms. In Systematic Biology, Vol. 51(2):199-216, 2002. Keywords: phylogenetic network, phylogeny, reconstruction, reticulogram. Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_SB.pdf.

InProceedings

5 Olivier Gauthier and François-Joseph Lapointe. A comparison of alternative methods for detecting reticulation events in phylogenetic analysis. In IFCS02, Pages 365-369, springer, 2002.         6 Dan Gusfield. Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions. In RECOMB02, 2002. Keywords: haplotyping, perfect, phylogeny. Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/acmhapre.pdf .         7 David Bryant and Vincent Moulton. Neighbor-Net: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. In WABI02, Vol. 2452:375-391 of LNCS, springer, 2002. Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network. Note: http://dx.doi.org/10.1007/3-540-45784-4_28.

Misc

8 Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. An error metric for phylogenetic networks. 2002. Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, tripartition distance. Note: Technical report TR-02-09, http://www.cs.unm.edu/~treport/tr/03-05/nakhleh.ps.gz.