r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
TLDR
R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times.Abstract:
Summary Estimating divergence times and rates of substitution from sequence data is plagued by the problem of rate variation between lineages. R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. Unlike most programs for rate inference or phylogenetics, r8s permits users to convert results to absolute rates and ages by constraining one or more node times to be fixed, minimum or maximum ages (using fossil or other evidence). Version 1.5 uses truncated Newton nonlinear optimization code with bound constraints, offering superior performance over previous versions. Availability The linux executable, C source code, sample data sets and user manual are available free at http://ginger.ucdavis.edu/r8s.read more
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ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
TL;DR: An r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees, which can read more tree file formats than other softwares, and support visualization of phylo, multiphylo, phylo4, phyla4d, obkdata and phyloseq tree objects defined in other r packages.
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A general species delimitation method with applications to phylogenetic placements
TL;DR: The Poisson tree processes (PTP) model is introduced to infer putative species boundaries on a given phylogenetic input tree and yields more accurate results than de novo species delimitation methods.
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Ancestral polyploidy in seed plants and angiosperms
Yuannian Jiao,Norman J. Wickett,Saravanaraj Ayyampalayam,André S. Chanderbali,Lena Landherr,Paula E. Ralph,Lynn P. Tomsho,Yi Hu,Haiying Liang,Pamela S. Soltis,Douglas E. Soltis,Sandra W. Clifton,Scott E. Schlarbaum,Stephan C. Schuster,Hong Ma,Jim Leebens-Mack,Claude W. dePamphilis +16 more
TL;DR: Comprehensive phylogenomic analyses of sequenced plant genomes and more than 12.6 million new expressed-sequence-tag sequences from phylogenetically pivotal lineages are used to elucidate two groups of ancient gene duplications, implicating two WGDs in ancestral lineages shortly before the diversification of extant seed plants and extant angiosperms.
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Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
TL;DR: The cross-platform software tool, TempEst (formerly known as Path-O-Gen), is introduced, for the visualization and analysis of temporally sampled sequence data and can be used to assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and identify sequences whose genetic divergence and sampling date are incongruent.
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RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
TL;DR: This paper presents the latest release of the program RAxML-III for rapid maximum likelihood-based inference of large evolutionary trees which allows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor.
References
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Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach
TL;DR: A semiparametric smoothing method is developed using penalized likelihood, a saturated model in which every lineage has a separate rate combined with a roughness penalty that discourages rates from varying too much across a phylogeny.
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