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Phylogenetics: New data, new challenges

Edited by Vincent Moulton, Mike Steel and Tandy Warnow

View all collections published in Algorithms for Molecular Biology.

  1. Recently one step mutation matrices were introduced to model the impact of substitutions on arbitrary branches of a phylogenetic tree on an alignment site. This concept works nicely for the four-state nucleoti...

    Authors: Mareike Fischer, Steffen Klaere, Minh Anh Thi Nguyen and Arndt von Haeseler

    Citation: Algorithms for Molecular Biology 2012 7:36

    Content type: Research

    Published on:

  2. The selection of an evolutionary model to best fit given molecular data is usually a heuristic choice. In his seminal book, J. Felsenstein suggested that certain linear equations satisfied by the expected prob...

    Authors: Marta Casanellas, Jesús Fernández-Sánchez and Anna M Kedzierska

    Citation: Algorithms for Molecular Biology 2012 7:33

    Content type: Research

    Published on:

  3. There are several common ways to encode a tree as a matrix, such as the adjacency matrix, the Laplacian matrix (that is, the infinitesimal generator of the natural random walk), and the matrix of pairwise dist...

    Authors: Frederick A Matsen and Steven N Evans

    Citation: Algorithms for Molecular Biology 2012 7:14

    Content type: Research

    Published on:

  4. Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing p...

    Authors: Lavanya Kannan and Ward C Wheeler

    Citation: Algorithms for Molecular Biology 2012 7:9

    Content type: Research

    Published on:

  5. We present optimal linear time algorithms for computing the Shapley values and 'heightened evolutionary distinctiveness' (HED) scores for the set of taxa in a phylogenetic tree. We demonstrate the efficiency o...

    Authors: Iain Martyn, Tyler S Kuhn, Arne O Mooers, Vincent Moulton and Andreas Spillner

    Citation: Algorithms for Molecular Biology 2012 7:6

    Content type: Research

    Published on:

  6. Supertree methods combine trees on subsets of the full taxon set together to produce a tree on the entire set of taxa. Of the many supertree methods, the most popular is MRP (Matrix Representation with Parsimo...

    Authors: Nam Nguyen, Siavash Mirarab and Tandy Warnow

    Citation: Algorithms for Molecular Biology 2012 7:3

    Content type: Research

    Published on: