MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Molecular Biology and Evolution - Tập 33 Số 7 - Trang 1870-1874 - 2016
Sudhir Kumar, Glen Stecher, Koichiro Tamura

Tóm tắt

Abstract We present the latest version of the Molecular Evolutionary Genetics Analysis (M ega ) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, M ega 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 M ega . 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 M ega 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 M ega 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.

Từ khóa


Tài liệu tham khảo

Edgar, 2004, Muscle: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, 5, 113., 10.1186/1471-2105-5-113

Filipski, 2014, Prospects for building large timetrees using molecular data with incomplete gene coverage among species, Mol Biol Evol, 31, 2542, 10.1093/molbev/msu200

Hedges, 2015, Tree of life reveals clock-like speciation and diversification, Mol Biol Evol, 32, 835, 10.1093/molbev/msv037

Kumar, 2012, M ega-cc : computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis, Bioinformatics, 28, 2685, 10.1093/bioinformatics/bts507

Kumar, 1994, M ega : molecular evolutionary genetics analysis software for microcomputers, Comput Appl Biosci, 10, 189

Quast, 2013, The SILVA ribosomal RNA gene database project: improved data processing and web-based tools, Nucleic Acids Res, 41, D590, 10.1093/nar/gks1219

Saitou, 1987, The neighbor-joining method—a new method for reconstructing phylogenetic trees, Mol Biol Evol, 4, 406

Tamura, 2012, Estimating divergence times in large molecular phylogenies, Proc Natl Acad Sci U S A, 109, 19333, 10.1073/pnas.1213199109

Tamura, 1993, Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees, Mol Biol Evol, 10, 512

Tamura, 2013, M ega 6: molecular evolutionary genetics analysis version 6.0, Mol Biol Evol, 30, 2725, 10.1093/molbev/mst197

Yilmaz, 2014, The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks, Nucleic Acids Res, 42, D643, 10.1093/nar/gkt1209

Zmasek, 2001, A simple algorithm to infer gene duplication and speciation events on a gene tree, Bioinformatics, 17, 821, 10.1093/bioinformatics/17.9.821