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Approximating the true evolutionary distance between two genomes
 in Proc. 7th SIAM Workshop on Algorithm Engineering & Experiments (ALENEXâ€™05), 121 (SIAM
, 2005
"... As more and more genomes are sequenced, evolutionary biologists are becoming increasingly interested in evolution at the level of whole genomes, in scenarios in which the genome evolves through insertions, duplications, deletions, and movements of genes along its chromosomes. In the mathematical mod ..."
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Cited by 36 (7 self)
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arbitrary genomes, but focus on approximating the true evolutionary distance rather than the edit distance. We present experimental results showing that our algorithm produces excellent estimates of the true evolutionary distance up to a (high) threshold of saturation; indeed, the distances thus produced
Abstract Approximating the True Evolutionary Distance Between Two Genomes
"... As more and more genomes are sequenced, evolutionary biologists are becoming increasingly interested in evolution at the level of whole genomes, in scenarios in which the genome evolves through insertions, duplications, deletions, and movements of genes along its chromosomes. In the mathematical mod ..."
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generalize our approach to handle duplications as well as insertions and thus enable the computation of distances between two arbitrary genomes; and our new algorithm approximates true evolutionary distances, as opposed to the less useful edit distances. We present experimental results showing that our
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 Guided Tour to Approximate String Matching
 ACM COMPUTING SURVEYS
, 1999
"... We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining t ..."
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Cited by 584 (38 self)
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We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining
Comparison of Multiobjective Evolutionary Algorithms: Empirical Results
, 2000
"... In this paper, we provide a systematic comparison of various evolutionary approaches to multiobjective optimization using six carefully chosen test functions. Each test function involves a particular feature that is known to cause difficulty in the evolutionary optimization process, mainly in conver ..."
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Cited by 605 (39 self)
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In this paper, we provide a systematic comparison of various evolutionary approaches to multiobjective optimization using six carefully chosen test functions. Each test function involves a particular feature that is known to cause difficulty in the evolutionary optimization process, mainly
MEGA5: Molecular evolutionary genetics analysis using maximum . . .
, 2011
"... Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version ..."
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Cited by 6858 (19 self)
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Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version
Property Testing and its connection to Learning and Approximation
"... We study the question of determining whether an unknown function has a particular property or is fflfar from any function with that property. A property testing algorithm is given a sample of the value of the function on instances drawn according to some distribution, and possibly may query the fun ..."
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Cited by 498 (68 self)
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the function on instances of its choice. First, we establish some connections between property testing and problems in learning theory. Next, we focus on testing graph properties, and devise algorithms to test whether a graph has properties such as being kcolorable or having a aeclique (clique of density ae
A Threshold of ln n for Approximating Set Cover
 JOURNAL OF THE ACM
, 1998
"... Given a collection F of subsets of S = f1; : : : ; ng, set cover is the problem of selecting as few as possible subsets from F such that their union covers S, and max kcover is the problem of selecting k subsets from F such that their union has maximum cardinality. Both these problems are NPhar ..."
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Cited by 778 (5 self)
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hard. We prove that (1 \Gamma o(1)) ln n is a threshold below which set cover cannot be approximated efficiently, unless NP has slightly superpolynomial time algorithms. This closes the gap (up to low order terms) between the ratio of approximation achievable by the greedy algorithm (which is (1 \Gamma
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
Improved Approximation Algorithms for Maximum Cut and Satisfiability Problems Using Semidefinite Programming
 Journal of the ACM
, 1995
"... We present randomized approximation algorithms for the maximum cut (MAX CUT) and maximum 2satisfiability (MAX 2SAT) problems that always deliver solutions of expected value at least .87856 times the optimal value. These algorithms use a simple and elegant technique that randomly rounds the solution ..."
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Cited by 1231 (13 self)
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We present randomized approximation algorithms for the maximum cut (MAX CUT) and maximum 2satisfiability (MAX 2SAT) problems that always deliver solutions of expected value at least .87856 times the optimal value. These algorithms use a simple and elegant technique that randomly rounds
Results 1  10
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