The Undirected Incomplete Perfect Phylogeny Problem

    Authors

    R. V. Satya;A. Mukherjee

    Comments

    Authors: contact us about adding a copy of your work at STARS@ucf.edu

    Abbreviated Journal Title

    IEEE-ACM Trans. Comput. Biol. Bioinform.

    Keywords

    Phylogenetics; perfect phylogeny; incomplete perfect phylogeny; haplotype inference; TIME ALGORITHM; SAMPLES; Biochemical Research Methods; Computer Science, Interdisciplinary; Applications; Mathematics, Interdisciplinary Applications; Statistics &; Probability

    Abstract

    The incomplete perfect phylogeny (IPP) problem and the incomplete perfect phylogeny haplotyping (IPPH) problem deal with constructing a phylogeny for a given set of haplotypes or genotypes with missing entries. The earlier approaches for both of these problems dealt with restricted versions of the problems, where the root is either available or can be trivially reconstructed from the data, or certain assumptions were made about the data. In this paper, we deal with the unrestricted versions of the problems, where the root of the phylogeny is neither available nor trivially recoverable from the data. Both IPP and IPPH problems have previously been proven to be NP-complete. Here, we present efficient enumerative algorithms that can handle practical instances of the problem. Empirical analysis on simulated data shows that the algorithms perform very well both in terms of speed and in terms accuracy of the recovered data.

    Journal Title

    Ieee-Acm Transactions on Computational Biology and Bioinformatics

    Volume

    5

    Issue/Number

    4

    Publication Date

    1-1-2008

    Document Type

    Article

    Language

    English

    First Page

    618

    Last Page

    629

    WOS Identifier

    WOS:000260433100013

    ISSN

    1545-5963

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