The Experts below are selected from a list of 147399 Experts worldwide ranked by ideXlab platform
Olivier Gascuel - One of the best experts on this subject based on the ideXlab platform.
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seaview version 4 a multiplatform graphical user interface for sequence alignment and Phylogenetic Tree building
Molecular Biology and Evolution, 2010Co-Authors: Manolo Gouy, Stéphane Guindon, Olivier GascuelAbstract:We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and Phylogenetic Tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood Tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating Phylogenetic Trees. In relation to the wide present offer of tools and algorithms for Phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.
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Sea view version 4: A multiplatform graphical user interface for sequence alignment and Phylogenetic Tree building
Molecular Biology and Evolution, 2010Co-Authors: Manolo Gouy, Stéphane Guindon, Olivier GascuelAbstract:We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and Phylogenetic Tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood Tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating Phylogenetic Trees. In relation to the wide present offer of tools and algorithms for Phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.
Simon Whelan - One of the best experts on this subject based on the ideXlab platform.
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characterizing the Phylogenetic Tree search problem
Systematic Biology, 2012Co-Authors: Daniel Money, Simon WhelanAbstract:Phylogenetic Trees are important in many areas of biological research, ranging from systematic studies to the methods used for genome annotation. Finding the best scoring Tree under any optimality criterion is an NP-hard problem, which necessitates the use of heuristics for Tree-search. Although Tree-search plays a major role in obtaining a Tree estimate, there remains a limited understanding of its characteristics and how the elements of the statistical inferential procedure interact with the algorithms used. This study begins to answer some of these questions through a detailed examination of maximum likelihood Tree-search on a wide range of real genome-scale data sets. We examine all 10,395 Trees for each of the 106 genes of an eight-taxa yeast phylogenomic data set, then apply different Tree-search algorithms to investigate their performance. We extend our findings by examining two larger genome-scale data sets and a large disparate data set that has been previously used to benchmark the performance of Tree-search programs. We identify several broad trends occurring during Tree-search that provide an insight into the performance of heuristics and may, in the future, aid their development. These trends include a tendency for the true maximum likelihood (best) Tree to also be the shortest Tree in terms of branch lengths, a weak tendency for Tree-search to recover the best Tree, and a tendency for Tree-search to encounter fewer local optima in genes that have a high information content. When examining current heuristics for Tree- search, we find that nearest-neighbor-interchange performs poorly, and frequently finds Trees that are significantly different from the best Tree. In contrast, subTree-pruning-and-regrafting tends to perform well, nearly always finding Trees that are not significantly different to the best Tree. Finally, we demonstrate that the precise implementation of a Tree-search strategy, including when and where parameters are optimized, can change the character of Tree-search, and that good strategies for Tree-search may combine existing Tree-search programs. (Algorithms; heuristics; maximum likelihood; NNI; Phylogenetics; SPR; Tree-search.)
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new approaches to Phylogenetic Tree search and their application to large numbers of protein alignments
Systematic Biology, 2007Co-Authors: Simon WhelanAbstract:Phylogenetic Tree estimation plays a critical role in a wide variety of molecular studies, including molecular sys- tematics, Phylogenetics, and comparative genomics. Finding the optimal Tree relating a set of sequences using score-based (optimality criterion) methods, such as maximum likelihood and maximum parsimony, may require all possible Trees to be considered, which is not feasible even for modest numbers of sequences. In practice, Trees are estimated using heuris- tics that represent a trade-off between topological accuracy and speed. I present a series of novel algorithms suitable for score-based Phylogenetic Tree reconstruction that demonstrably improve the accuracy of Tree estimates while maintaining high computational speeds. The heuristics function by allowing the efficient exploration of large numbers of Trees through novel hill-climbing and resampling strategies. These heuristics, and other computational approximations, are implemented for maximum likelihood estimation of Trees in the program Leaphy, and its performance is compared to other popular phy- logenetic programs. Trees are estimated from 4059 different protein alignments using a selection of Phylogenetic programs and the likelihoods of the Tree estimates are compared. Trees estimated using Leaphy are found to have equal to or better likelihoods than Trees estimated using other Phylogenetic programs in 4004 (98.6%) families and provide a unique best Tree that no other program found in 1102 (27.1%) families. The improvement is particularly marked for larger families (80 to 100 sequences), where Leaphy finds a unique best Tree in 81.7% of families. (Algorithms; evolution; Phylogenetic Tree inference; Tree estimation heuristics.)
Stéphane Guindon - One of the best experts on this subject based on the ideXlab platform.
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seaview version 4 a multiplatform graphical user interface for sequence alignment and Phylogenetic Tree building
Molecular Biology and Evolution, 2010Co-Authors: Manolo Gouy, Stéphane Guindon, Olivier GascuelAbstract:We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and Phylogenetic Tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood Tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating Phylogenetic Trees. In relation to the wide present offer of tools and algorithms for Phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.
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Sea view version 4: A multiplatform graphical user interface for sequence alignment and Phylogenetic Tree building
Molecular Biology and Evolution, 2010Co-Authors: Manolo Gouy, Stéphane Guindon, Olivier GascuelAbstract:We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and Phylogenetic Tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood Tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating Phylogenetic Trees. In relation to the wide present offer of tools and algorithms for Phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.
Manolo Gouy - One of the best experts on this subject based on the ideXlab platform.
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seaview version 4 a multiplatform graphical user interface for sequence alignment and Phylogenetic Tree building
Molecular Biology and Evolution, 2010Co-Authors: Manolo Gouy, Stéphane Guindon, Olivier GascuelAbstract:We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and Phylogenetic Tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood Tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating Phylogenetic Trees. In relation to the wide present offer of tools and algorithms for Phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.
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Sea view version 4: A multiplatform graphical user interface for sequence alignment and Phylogenetic Tree building
Molecular Biology and Evolution, 2010Co-Authors: Manolo Gouy, Stéphane Guindon, Olivier GascuelAbstract:We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and Phylogenetic Tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood Tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating Phylogenetic Trees. In relation to the wide present offer of tools and algorithms for Phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available at http://pbil.univ-lyon1.fr/software/seaview.
Frederick A Matsen - One of the best experts on this subject based on the ideXlab platform.
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systematic exploration of the high likelihood set of Phylogenetic Tree topologies
Systematic Biology, 2019Co-Authors: Chris Whidden, Brian C Claywell, Thayer Fisher, Andrew F Magee, Mathieu Fourment, Frederick A MatsenAbstract:: Bayesian Markov chain Monte Carlo explores Tree space slowly, in part because it frequently returns to the same Tree topology. An alternative strategy would be to explore Tree space systematically, and never return to the same topology. In this paper, we present an efficient parallelized method to map out the high likelihood set of Phylogenetic Tree topologies via systematic search, which we show to be a good approximation of the high posterior set of Tree topologies on the data sets analyzed. Here "likelihood" of a topology refers to the Tree likelihood for the corresponding Tree with optimized branch lengths. We call this method "Phylogenetic topographer" (PT). The PT strategy is very simple: starting in a number of local topology maxima (obtained by hill-climbing from random starting points), explore out using local topology rearrangements, only continuing through topologies that are better than some likelihood threshold below the best observed topology. We show that the normalized topology likelihoods are a useful proxy for the Bayesian posterior probability of those topologies. By using a non-blocking hash table keyed on unique representations of Tree topologies, we avoid visiting topologies more than once across all concurrent threads exploring Tree space. We demonstrate that PT can be used directly to approximate a Bayesian consensus Tree topology. When combined with an accurate means of evaluating per-topology marginal likelihoods, PT gives an alternative procedure for obtaining Bayesian posterior distributions on Phylogenetic Tree topologies.
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systematic exploration of the high likelihood set of Phylogenetic Tree topologies
arXiv: Populations and Evolution, 2018Co-Authors: Chris Whidden, Brian C Claywell, Thayer Fisher, Andrew F Magee, Mathieu Fourment, Frederick A MatsenAbstract:Bayesian Markov chain Monte Carlo explores Tree space slowly, in part because it frequently returns to the same Tree topology. An alternative strategy would be to explore Tree space systematically, and never return to the same topology. In this paper, we present an efficient parallelized method to map out the high likelihood set of Phylogenetic Tree topologies via systematic search, which we show to be a good approximation of the high posterior set of Tree topologies. Here `likelihood' of a topology refers to the Tree likelihood for the corresponding Tree with optimized branch lengths. We call this method `Phylogenetic topographer' (PT). The PT strategy is very simple: starting in a number of local topology maxima (obtained by hill-climbing from random starting points), explore out using local topology rearrangements, only continuing through topologies that are better than than some likelihood threshold below the best observed topology. We show that the normalized topology likelihoods are a useful proxy for the Bayesian posterior probability of those topologies. By using a non-blocking hash table keyed on unique representations of Tree topologies, we avoid visiting topologies more than once across all concurrent threads exploring Tree space. We demonstrate that PT can be used directly to approximate a Bayesian consensus Tree topology. When combined with an accurate means of evaluating per-topology marginal likelihoods, PT gives an alternative procedure for obtaining Bayesian posterior distributions on Phylogenetic Tree topologies.
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quantifying mcmc exploration of Phylogenetic Tree space
arXiv: Populations and Evolution, 2014Co-Authors: Chris Whidden, Frederick A MatsenAbstract:In order to gain an understanding of the effectiveness of Phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this paper we investigate this problem on Phylogenetic Tree topologies with a metric that is especially well suited to the task: the subTree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move between Trees in common Phylogenetic MCMC implementations. We develop a novel graph-based approach to analyze Tree posteriors and find that the SPR metric is much more informative than simpler metrics that are unrelated to MCMC moves. In doing so we show conclusively that topological peaks do occur in Bayesian Phylogenetic posteriors from real data sets as sampled with standard MCMC approaches, investigate the efficiency of Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks, and show that conditional clade distribution (CCD) can have systematic problems when there are multiple peaks.
