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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
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 newExpand
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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting treeExpand
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Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing anExpand
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SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
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 userExpand
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A Simple, Fast, and Accurate Method to Estimate Large Phylogenies by Maximum Likelihood
—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 newExpand
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Phylogeny.fr: robust phylogenetic analysis for the non-specialist
TLDR
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, phylogenetic reconstruction and the graphical representation of the inferred tree. Expand
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Estimating maximum likelihood phylogenies with PhyML.
Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complexExpand
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Modeling the site-specific variation of selection patterns along lineages.
The unambiguous footprint of positive Darwinian selection in protein-coding DNA sequences is revealed by an excess of nonsynonymous substitutions over synonymous substitutions compared with theExpand
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Genomics, biogeography, and the diversification of placental mammals
Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have notExpand
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Efficient biased estimation of evolutionary distances when substitution rates vary across sites.
This paper deals with phylogenetic inference when the variability of substitution rates across sites (VRAS) is modeled by a gamma distribution. We show that underestimating VRAS, which results inExpand
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