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Simple Reconstruction of Binary NearPerfect Phylogenetic Trees
 In proc International Workshop on Bioinformatics Research and Applications
, 2006
"... Abstract. We consider the problem of reconstructing nearperfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states that is computati ..."
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Cited by 11 (7 self)
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Abstract. We consider the problem of reconstructing nearperfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states
FPT Algorithms for Binary NearPerfect Phylogenetic Trees
, 2005
"... We consider the problem of reconstructing nearperfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states that is computationally eff ..."
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Cited by 2 (0 self)
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We consider the problem of reconstructing nearperfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states that is computationally
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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with the data set exists it can be constructed in linear time. However, real data sets often do not admit perfect phylogenies. In this paper, we consider the problem of reconstructing nearperfect phylogenetic trees (referred to as BNPP). A nearperfect phylogeny relaxes the perfect phylogeny assumption
A New Algorithm for the Reconstruction of NearPerfect Binary Phylogenetic Trees
, 2005
"... In this paper, we consider the problem of reconstructing nearperfect phylogenetic trees using binary characters. A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree. The algorithm for reconstructing a perfect phylogeny for binary characters is computationa ..."
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In this paper, we consider the problem of reconstructing nearperfect phylogenetic trees using binary characters. A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree. The algorithm for reconstructing a perfect phylogeny for binary characters
Algorithms for Efficient NearPerfect Phylogenetic Tree Reconstruction in Theory and Practice
"... Abstract—We consider the problem of reconstructing nearperfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states that is computatio ..."
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Cited by 5 (2 self)
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Abstract—We consider the problem of reconstructing nearperfect phylogenetic trees using binary character states (referred to as BNPP). A perfect phylogeny assumes that every character mutates at most once in the evolutionary tree, yielding an algorithm for binary character states
Application of Phylogenetic Networks in Evolutionary Studies
 SUBMITTED TO MBE 2005
, 2005
"... The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evoluti ..."
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Cited by 867 (15 self)
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The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
, 2003
"... The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The ..."
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Cited by 2109 (30 self)
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. The core of this method is a simple hillclimbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distancebased method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment
The ubiquitous Btree
 ACM Computing Surveys
, 1979
"... Btrees have become, de facto, a standard for file organization. File indexes of users, dedicated database systems, and generalpurpose access methods have all been proposed and nnplemented using Btrees This paper reviews Btrees and shows why they have been so successful It discusses the major var ..."
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Cited by 653 (0 self)
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Btrees have become, de facto, a standard for file organization. File indexes of users, dedicated database systems, and generalpurpose access methods have all been proposed and nnplemented using Btrees This paper reviews Btrees and shows why they have been so successful It discusses the major
Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates over Sites: Approximate Methods
 J. Mol. Evol
, 1994
"... Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called ..."
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Cited by 540 (28 self)
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Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called
Additive Approximation for NearPerfect Phylogeny Construction
"... We study the problem of constructing phylogenetic trees for a given set of species. The problem is formulated as that of finding a minimum Steiner tree on n points over the Boolean hypercube of dimension d. It is known that an optimal tree can be found in linear time [1] if the given dataset has a ..."
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perfect phylogeny, i.e. cost of the optimal phylogeny is exactly d. Moreover, if the data has a nearperfect phylogeny, i.e. the cost of the optimal Steiner tree is d + q, it is known [2] that an exact solution can be found in running time which is polynomial in the number of species and d, yet
Results 1  10
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147,421