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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by . . .
, 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 851 (14 self)
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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 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 of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximumlikelihood programs and much higher than the performance of distancebased and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximumlikelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distancebased and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/. [Algorithm; computer simulations; maximum likelihood; phylogeny; rbcL; RDPII project.] The size of homologous sequence data sets has increased dramatically in recent years, and many of these data sets now involve several hundreds of taxa. Moreover, current probabilist...
TREEVIEW: An application to display phylogenetic trees on personal computers
, 1996
"... Introduction TREEVIEW is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two commonest personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1 ..."
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Cited by 558 (1 self)
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Introduction TREEVIEW is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two commonest personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers. Furthermore, they require the user to load a data set before any trees can be displayed which is inconvenient if the user simply wants to view the trees. More portable programs, such as DRAWGRAM and DRAWTREE in the PHYLIP package (Felsenstein, 1993) can run on both MacOS and Windows computers, but make little, if any use of the graphical interface features available under those operating systems. TREEVIEW runs as a native application
Raxmliii: a fast program for maximum likelihoodbased inference of large phylogenetic trees
 Bioinformatics
, 2005
"... Motivation: The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to ..."
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Cited by 114 (12 self)
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Motivation: The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods such as parsimony or neighbor joining. Due to the combinatorial and computational complexity the size of trees which can be computed on a Biologist’s PC workstation within reasonable time is limited to trees containing approximately 100 taxa. Results: In this paper we present the latest release of our program RAxMLIII for rapid maximum likelihoodbased inference of large evolutionary trees which allows for computation of 1.000taxon trees in less than 24 hours on a single PC processor. We compare RAxMLIII to the currently fastest implementations for maximum likelihood and bayesian inference: PHYML and MrBayes. Whereas RAxMLIII performs worse than PHYML and MrBayes on synthetic data it clearly outperforms both programs on all real data alignments used in terms of speed and final likelihood values. Availability & Supplementary Information: RAxMLIII including all alignments and final trees mentioned in this paper is freely available as open source code at
Fast and Accurate Phylogeny Reconstruction Algorithms Based on the MinimumEvolution Principle
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 2002
"... The Minimum Evolution (ME) approach to phylogeny estimation has been shown to be statistically consistent when it is used in conjunction with ordinary leastsquares (OLS) fitting of a metric to a tree structure. The traditional approach to using ME has been to start with the Neighbor Joining (NJ) to ..."
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Cited by 57 (5 self)
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The Minimum Evolution (ME) approach to phylogeny estimation has been shown to be statistically consistent when it is used in conjunction with ordinary leastsquares (OLS) fitting of a metric to a tree structure. The traditional approach to using ME has been to start with the Neighbor Joining (NJ) topology for a given matrix and then do a topological search from that starting point. The first stage requires O(n³) time, where n is the number of taxa, while the current implementations of the second are in O(p n³) or more, where p is the number of swaps performed by the program. In this paper, we examine a greedy approach to minimum evolution which produces a starting topology in O(n²) time. Moreover, we provide an algorithm that searches for the best topology using nearest neighbor interchanges (NNIs), where the cost of doing p NNIs is O(n² C p n), i.e., O(n²) in practice because p is always much smaller than n. The Greedy Minimum Evolution (GME) algorithm, when used in combination with NNIs, produces trees which are fairly close to NJ trees in terms of topological accuracy. We also examine ME under a balanced weighting scheme, where sibling subtrees have equal weight, as opposed to the standard “unweighted ” OLS, where
Inferring phylogeny despite incomplete lineage sorting
 Syst. Biol
, 2006
"... Abstract.—It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome these difficulties by explicitly considering the processes that produce them. Here we explore approaches to ..."
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Cited by 55 (1 self)
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Abstract.—It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome these difficulties by explicitly considering the processes that produce them. Here we explore approaches to phylogenetic inference designed to consider retention and sorting of ancestral polymorphism. We examine how the reconstructability of a species (or population) phylogeny is affected by (a) the number of loci used to estimate the phylogeny and (b) the number of individuals sampled per species. Even in difficult cases with considerable incomplete lineage sorting (times between divergences less than 1 Ne generations), we found the reconstructed species trees matched the "true " species trees in at least three out of five partitions, as long as a reasonable number of individuals per species were sampled. We also studied the tradeoff between sampling more loci versus more individuals. Although increasing the number of loci gives more accurate trees for a given sampling effort with deeper species trees (e.g., total depth of 10 Nc generations), sampling more individuals often gives better results than sampling more loci with shallower species trees (e.g., depth = 1 Ne). Taken together, these results demonstrate that gene sequences retain enough signal to achieve an accurate estimate of phylogeny despite widespread incomplete lineage sorting. Continued improvement in our methods to reconstruct phylogeny near the species level will require a shift to a compound model that considers not only nucleotide or character state substitutions, but also the population genetics processes of lineage sorting. [Coalescence; divergence; population; speciation.]
Phylogenomic inference of protein molecular function: advances and challenges
 Bioinformatics
, 2004
"... Motivation: Protein families evolve a multiplicity of functions through gene duplication, speciation and other processes. As a number of studies have shown, standard methods of protein function prediction produce systematic errors on these data. Phylogenomic analysis—combining phylogenetic tree cons ..."
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Cited by 51 (2 self)
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Motivation: Protein families evolve a multiplicity of functions through gene duplication, speciation and other processes. As a number of studies have shown, standard methods of protein function prediction produce systematic errors on these data. Phylogenomic analysis—combining phylogenetic tree construction, integration of experimental data and differentiation of orthologs and paralogs—has been proposed to address these errors and improve the accuracy of functional classification. The explicit integration of structure prediction and analysis in this framework, which we call structural phylogenomics, provides additional insights into protein superfamily evolution. Results: Results of protein functional classification using phylogenomic analysis show fewer expected false positives overall than when pairwise methods of functional classification are employed. We present an overview of the motivations and fundamental principles of phylogenomic analysis, new methods developed for the key tasks, benchmark datasets for these tasks (when available) and suggest procedures to increase accuracy. We also discuss some of the methods used in the Celera Genomics highthroughput phylogenomic classification of the human genome. Availability: Software tools from the Berkeley Phylogenomics Group are available at
Reconstructing reticulate evolution in species  theory and practice
 In Proc. of 8’th Annual International Conference on Computational Molecular Biology
, 2004
"... We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of Wayne Maddison’s approach in his seminal 1997 paper. Our first method is a polynomial time algorithm for constructing ph ..."
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Cited by 46 (7 self)
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We present new methods for reconstructing reticulate evolution of species due to events such as horizontal transfer or hybrid speciation; both methods are based upon extensions of Wayne Maddison’s approach in his seminal 1997 paper. Our first method is a polynomial time algorithm for constructing phylogenetic networks from two gene trees contained inside the network. We allow the network to have an arbitrary number of reticulations, but we limit the reticulation in the network so that the cycles in network are nodedisjoint (“galled”). Our second method is a polynomial time algorithm for constructing networks with one reticulation, where we allow for errors in the estimated gene trees. Using simulations, we demonstrate improved performance of this method over both NeighborNet and Maddison’s method. 1
Cytokinesis in the Arabidopsis embryo involves the syntaxinrelated KNOLLE gene product
 Cell
, 1996
"... events in different pathways. ..."
RecIDCM3: A fast algorithmic technique for reconstructing large phylogenetic trees
 In Proc. IEEE Computer Society Bioinformatics Conference (CSB 2004
, 2004
"... ..."
Multiplelocus variablenumber tandem repeat analysis reveals genetic relationships within Bacillus anthracis
 J
"... This article cites 22 articles, 17 of which can be accessed free ..."
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Cited by 33 (6 self)
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This article cites 22 articles, 17 of which can be accessed free