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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. Content type: Research

    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

    Published on:

  2. Content type: Research

    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

    Published on:

  3. Content type: Research

    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

    Published on:

  4. Content type: Research

    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

    Published on:

  5. Content type: Research

    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

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  6. Content type: Research

    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

    Published on:

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