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      Contrasting effects of phylogenetic relatedness on plant invader success in experimental grassland communities

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          MUSCLE: multiple sequence alignment with high accuracy and high throughput.

          R. C. Edgar (2004)
          We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
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            Bayesian Phylogenetics with BEAUti and the BEAST 1.7

            Alexei J. Drummond, Marc Suchard, Dong-jie Xie … (2012)
            Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7, which implements a family of Markov chain Monte Carlo (MCMC) algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. This package includes an enhanced graphical user interface program called Bayesian Evolutionary Analysis Utility (BEAUti) that enables access to advanced models for molecular sequence and phenotypic trait evolution that were previously available to developers only. The package also provides new tools for visualizing and summarizing multispecies coalescent and phylogeographic analyses. BEAUti and BEAST 1.7 are open source under the GNU lesser general public license and available at http://beast-mcmc.googlecode.com and http://beast.bio.ed.ac.uk
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              Picante: R tools for integrating phylogenies and ecology.

              Steven W Kembel, Peter D Cowan, Matthew R Helmus … (2010)
              Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).
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                Author and article information

                Journal
                Title: Journal of Applied Ecology
                Abbreviated Title: J Appl Ecol
                Publisher: Wiley-Blackwell
                ISSN: 00218901
                Publication date Created: February 2015
                Publication date (Print): February 2015
                Volume: 52
                Issue: 1
                Pages: 89-99
                Article
                DOI: 10.1111/1365-2664.12365
                SO-VID: 31e035dc-9d7f-4b1b-9681-82c1b44f9300
                Copyright © © 2015
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                http://doi.wiley.com/10.1002/tdm_license_1.1

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