MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Abstract

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.

Keywords: evolution.; gene families; software; timetree.

F ig . 1.

Time and memory requirements for phylogenetic analyses using the NJ method ( A , B ) and the ML analysis ( C , D ). For NJ analysis, we used the Tamura–Nei (1993) model, uniform rates of evolution among sites, and pairwise deletion option to deal with the missing data. Time usage increases polynomially with the number of sequences (third degree polynomial, R  ² =  1), as does the peak memory used ( R  ² =  1) ( A , B ). The same model and parameters were used for ML tree inference, where the time taken and the memory needs increased linearly with the number of sequences. For ML analysis, the SPR (Subtree–Pruning–Regrafting) heuristic was used for tree searching and all 5,287 sites in the sequence alignment were included. All the analyses were performed on a Dell Optiplex 9010 computer with an Intel Core-i7-3770 3.4 GHz processor, 20 GB of RAM, NVidia GeForce GT 640 graphics card, and a 64-bit Windows 7 Enterprise operating system.

F ig . 2.

The Gene Duplication Wizard ( A ) to guide users through the process of searching gene duplication events in a gene family tree. In the first step, the user loads a gene tree from a Newick formatted text file. Second, species associated with sequences are specified using a graphical interface. In the third step, the user has the option to load a trusted species tree, in which case it will be possible to identify all duplication events in the gene tree, from a Newick file. Fourth, the user has the option to specify the root of the gene tree in a graphical interface. If the user provides a trusted species tree, then they must designate the root of that tree. Finally, the user launches the analysis and the results are displayed in the Tree Explorer window (see fig. 3 ).

F ig . 3.

Tree Explorer window with gene duplications marked with closed blue diamonds and speciation events, if a trusted species tree is provided, are identified by open red diamonds (see fig. 2 legend for more information).