On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa

  title={On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa},
  author={Merc{\`e} Llabr{\'e}s and Jairo Rocha and Francesc Rossell{\'o} and Gabriel Valiente},
  journal={Journal of Mathematical Biology},
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was recently introduced. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence… 
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The original description of AncestralBuild can be modified so that the running time is as fast as the current fastest running time for Build, a polynomial-time algorithm for deciding the compatibility of a collection of source trees in which some of the interior nodes are also labeled by taxa.
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The research work presented in this manuscript is of algorithmic kind: it is mainly composed of polynomial, fixed parameter and approximation algorithms, while hardness results are also mentioned.
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Parsimony analysis of a matrix representingRooted phylogenetic trees as matrices in which the rows correspond to termini, and columns correspond to internal nodes will fully recover the topology of the original tree.
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  • Mathematics, Computer Science
    SODA '93
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This paper will present an O(nk) algorithm for the tree compatibility problem, and demonstrate that this algorithm is superior to the other algorithms for perfect phylogeny problem for many realistic cases, such as when the species are defined by molecular data such as amino-acid sequences.
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