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115
Early Eukaryote Evolution Based on Mitochondrial Gene Order Breakpoints
 Journal of Computational Biology
, 2004
"... The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the "median problem for breakpoints"; this solution can then be incorporated into a routine for ..."
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Cited by 19 (6 self)
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for estimating optimal gene orders for all the ancestral genomes in a fixed phylogeny. For the di#cult (and most prevalent) case where the genomes contain partially di#erent sets of genes, we present a general heuristic for the median problem for induced breakpoints. A fixedphylogeny optimization based
Fixed Topology Alignment with Recombination
"... In this paper, we study a new version of multiple sequence alignment, fixed topology alignment with recombination. We show that it can not be approximated within any constant ratio unless P = NP . For a more restricted version, we show that the problem is MAXSNPhard. This implies that there is ..."
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Cited by 6 (1 self)
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In this paper, we study a new version of multiple sequence alignment, fixed topology alignment with recombination. We show that it can not be approximated within any constant ratio unless P = NP . For a more restricted version, we show that the problem is MAXSNPhard. This implies
A PolynomialTime Algorithm for the Phylogeny Problem when the Number of Character States is Fixed
 SIAM J. COMPUT
, 1993
"... We present a polynomialtime algorithm for determining whether a set of species, described by the characters they exhibit, has a phylogenetic tree, assuming the maximum number of possible states for a character is fixed. This solves an open problem posed by Kannan and Warnow. Our result should be co ..."
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Cited by 6 (0 self)
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We present a polynomialtime algorithm for determining whether a set of species, described by the characters they exhibit, has a phylogenetic tree, assuming the maximum number of possible states for a character is fixed. This solves an open problem posed by Kannan and Warnow. Our result should
Fixed parameter tractability of binary nearperfect phylogenetic tree reconstruction
 International Colloquium on Automata, Languages and Programming
, 2006
"... Abstract. We consider the problem of finding a Steiner minimum tree in a hypercube. Specifically, given n terminal vertices in an m dimensional cube and a parameter q, we compute the Steiner minimum tree in time O(72 q + 8 q nm 2), under the assumption that the length of the minimum Steiner tree is ..."
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Cited by 18 (7 self)
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is at most m + q. This problem has extensive applications in taxonomy and biology. The Steiner tree problem in hypercubes is equivalent to the phylogeny (evolutionary tree) reconstruction problem under the maximum parsimony criterion, when each taxon is defined over binary states. The taxa, character set
A POLYNOMIALTIME ALGORITHM FOR NEARPERFECT PHYLOGENY ∗
"... Abstract. A parameterized version of the Steiner tree problem in phylogeny is defined, where the parameter measures the amount by which a phylogeny differs from “perfection. ” This problem is shown to be solvable in polynomial time for any fixed value of the parameter. ..."
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Abstract. A parameterized version of the Steiner tree problem in phylogeny is defined, where the parameter measures the amount by which a phylogeny differs from “perfection. ” This problem is shown to be solvable in polynomial time for any fixed value of the parameter.
Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance
 J. Bioinform. Comput. Biol
, 2004
"... A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the appearance frequency of oligopeptides of a fixed length (up to � �) in their proteomes. This is a method without fine adj ..."
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Cited by 32 (10 self)
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A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the appearance frequency of oligopeptides of a fixed length (up to � �) in their proteomes. This is a method without fine
Approximation Algorithms for the FixedTopology Phylogenetic Number Problem
, 1999
"... . In the `phylogeny problem, one wishes to construct an evolutionary tree for a set of species represented by characters, in which each state of each character induces no more than ` connected components. We consider the fixedtopology version of this problem for fixedtopologies of arbitrary degr ..."
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Cited by 1 (1 self)
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. In the `phylogeny problem, one wishes to construct an evolutionary tree for a set of species represented by characters, in which each state of each character induces no more than ` connected components. We consider the fixedtopology version of this problem for fixedtopologies of arbitrary
Haplotyping with missing data via perfect path phylogenies
, 2007
"... Computational methods for inferring haplotype information from genotype data are used in studying the association between genomic variation and medical condition. Recently, Gusfield proposed a haplotype inference method that is based on perfect phylogeny principles. A fundamental problem arises when ..."
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Cited by 7 (3 self)
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phylogeny is sought. Searching for perfect path phylogenies is strongly motivated by the characteristics of human genotype data: 70 % of real instances that admit a perfect phylogeny also admit a perfect path phylogeny. Our main result is a fixedparameter algorithm for haplotyping with missing data via
Application of Smodels in Quartet Based Phylogeny Construction
"... Abstract. Evolution is an important subarea of study in biological science, where given a set of taxa, the goal is to reconstruct their evolutionary history, or phylogeny. One very recent approach is to predict a local phylogeny for every subset of 4 taxa, called a quartet topology, and then to ass ..."
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Abstract. Evolution is an important subarea of study in biological science, where given a set of taxa, the goal is to reconstruct their evolutionary history, or phylogeny. One very recent approach is to predict a local phylogeny for every subset of 4 taxa, called a quartet topology
Algorithms for Phylogeny Reconstruction in a New Mathematical Model
"... The evolutionary history of a set of species is represented by a tree, called a phylogenetic tree or phylogeny, whose structure depends on precise biological assumptions about the evolution of species. Problems related to phylogeny reconstruction (i.e., finding a tree representation of informati ..."
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The evolutionary history of a set of species is represented by a tree, called a phylogenetic tree or phylogeny, whose structure depends on precise biological assumptions about the evolution of species. Problems related to phylogeny reconstruction (i.e., finding a tree representation
Results 11  20
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115