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      MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

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          Abstract

          The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

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          MEGA2: molecular evolutionary genetics analysis software

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            MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis.

            There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. http://www.megasoftware.net/.
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              Author and article information

              Journal
              Molecular Biology and Evolution
              Oxford University Press (OUP)
              0737-4038
              1537-1719
              June 2018
              June 01 2018
              May 02 2018
              June 2018
              June 01 2018
              May 02 2018
              : 35
              : 6
              : 1547-1549
              Affiliations
              [1 ]Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
              [2 ]Department of Biology, Temple University, Philadelphia, PA
              [3 ]Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
              [4 ]Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Japan
              [5 ]Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
              Article
              10.1093/molbev/msy096
              5967553
              29722887
              © 2018

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