Blog
About

  • Record: found
  • Abstract: not found
  • Article: not found

Phylogenomic Data Yield New and Robust Insights into the Phylogeny and Evolution of Weevils

Read this article at

ScienceOpenPublisher
Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Related collections

      Most cited references 77

      • Record: found
      • Abstract: found
      • Article: not found

      MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

      We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
        Bookmark
        • Record: found
        • Abstract: found
        • Article: not found

        MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.

        We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict gene duplication events in gene family trees. The 64-bit Mega is made available in two interfaces: graphical and command line. The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OS X. The command line Mega is available as native applications for Windows, Linux, and Mac OS X. They are intended for use in high-throughput and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

          Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
            Bookmark

            Author and article information

            Affiliations
            [1 ]Department of Biological Sciences, University of Memphis, Memphis, TN
            [2 ]Department of Scientific Computing, Florida State University, Tallahassee, FL
            [3 ]Department of Biological Science, Florida State University, Tallahassee, FL
            [4 ]Museum of Comparative Zoology, Harvard University, Cambridge, MA
            [5 ]CONICET, División Entomología, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
            [6 ]CSIRO, Australian National Insect Collection, Canberra, ACT, Australia
            Journal
            Molecular Biology and Evolution
            Oxford University Press (OUP)
            0737-4038
            1537-1719
            April 2018
            April 2018
            April 01 2018
            December 26 2017
            : 35
            : 4
            : 823-836
            10.1093/molbev/msx324
            © 2017

            http://academic.oup.com/journals/pages/about_us/legal/notices

            Comments

            Comment on this article