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208,764
UniFrac: a new phylogenetic method for comparing microbial communities
 APPL. ENVIRON
, 2005
"... ..."
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 887 (15 self)
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evolution proceeds in a treelike manner, analysis of the data may not be best served by using methods that enforce a tree structure, but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when
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 557 (29 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
PAML: a program package for phylogenetic analysis by maximum likelihood
 COMPUT APPL BIOSCI 13:555–556
, 1997
"... PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the tr ..."
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Cited by 1459 (17 self)
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PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree
PAUP*: Phylogenetic Analysis Using Parsimony (and other methods) 4.0.b5
, 2001
"... This documentation is currently under construction, therefore, we cannot guarantee the accuracy of the information described herein. A much more userfriendly manual is in progress. Revisions will be made available to registered users over the World Wide Web at ..."
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Cited by 5090 (6 self)
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This documentation is currently under construction, therefore, we cannot guarantee the accuracy of the information described herein. A much more userfriendly manual is in progress. Revisions will be made available to registered users over the World Wide Web at
A New Method for Solving Hard Satisfiability Problems
 AAAI
, 1992
"... We introduce a greedy local search procedure called GSAT for solving propositional satisfiability problems. Our experiments show that this procedure can be used to solve hard, randomly generated problems that are an order of magnitude larger than those that can be handled by more traditional approac ..."
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Cited by 730 (21 self)
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We introduce a greedy local search procedure called GSAT for solving propositional satisfiability problems. Our experiments show that this procedure can be used to solve hard, randomly generated problems that are an order of magnitude larger than those that can be handled by more traditional approaches such as the DavisPutnam procedure or resolution. We also show that GSAT can solve structured satisfiability problems quickly. In particular, we solve encodings of graph coloring problems, Nqueens, and Boolean induction. General application strategies and limitations of the approach are also discussed. GSAT is best viewed as a modelfinding procedure. Its good performance suggests that it may be advantageous to reformulate reasoning tasks that have traditionally been viewed as theoremproving problems as modelfinding tasks.
Ensemble Methods in Machine Learning
 MULTIPLE CLASSIFIER SYSTEMS, LBCS1857
, 2000
"... Ensemble methods are learning algorithms that construct a set of classifiers and then classify new data points by taking a (weighted) vote of their predictions. The original ensemble method is Bayesian averaging, but more recent algorithms include errorcorrecting output coding, Bagging, and boostin ..."
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Cited by 625 (3 self)
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Ensemble methods are learning algorithms that construct a set of classifiers and then classify new data points by taking a (weighted) vote of their predictions. The original ensemble method is Bayesian averaging, but more recent algorithms include errorcorrecting output coding, Bagging
Boosting the margin: A new explanation for the effectiveness of voting methods
 IN PROCEEDINGS INTERNATIONAL CONFERENCE ON MACHINE LEARNING
, 1997
"... One of the surprising recurring phenomena observed in experiments with boosting is that the test error of the generated classifier usually does not increase as its size becomes very large, and often is observed to decrease even after the training error reaches zero. In this paper, we show that this ..."
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Cited by 897 (52 self)
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that techniques used in the analysis of Vapnik’s support vector classifiers and of neural networks with small weights can be applied to voting methods to relate the margin distribution to the test error. We also show theoretically and experimentally that boosting is especially effective at increasing the margins
Suffix arrays: A new method for online string searches
, 1991
"... A new and conceptually simple data structure, called a suffix array, for online string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees is that ..."
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Cited by 835 (0 self)
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A new and conceptually simple data structure, called a suffix array, for online string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees
The Hungarian method for the assignment problem
 Naval Res. Logist. Quart
, 1955
"... Assuming that numerical scores are available for the performance of each of n persons on each of n jobs, the "assignment problem" is the quest for an assignment of persons to jobs so that the sum of the n scores so obtained is as large as possible. It is shown that ideas latent in the work ..."
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Cited by 1259 (0 self)
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in the work of two Hungarian mathematicians may be exploited to yield a new method of solving this problem. 1.
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