Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-2739

Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
Molecular Biology and Evolution (Impact Factor: 9.11). 05/2011; 28(10):2731-9. DOI: 10.1093/molbev/msr121
Source: PubMed


Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.

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    • "The output of GenDiff generates a minimum convex polygon that encompasses all sampling sites within a genetic group, where warmer colors represent areas with stronger local genetic differentiation. Genetic distances between all mitochondrial ND2-alignment pairs were estimated assuming the K2P model in MEGA 4.0 (Tamura et al., 2011), using the pairwise-deletion option. In Local- Diff we implemented the following parameters: two fictional neighboring populations in the vicinity of each sampled site, and a geographic distance between the neighbors and the sampling sites of 0.1 km. "
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    • "All polymorphic sites with a probability of <0.6 were coded in both alleles with the appropriate IUPAC ambiguity code. Mega v. 5.0 (Tamura et al., 2011) was used to estimate uncorrected p-distances between lineages. Specimens used in this study, corresponding GenBank accession numbers and localities are provided as Supplementary Material in Table S1. "
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    • "phylogeny was established on a subset of species (ca 40%) using nucleotide sequence data for the rbcL gene extracted from the Gen- Bank database. This phylogeny was obtained using the BEAST 1.7 software (Drummond et al., 2012) after alignment of the sequences in Mega 5.1 (Tamura et al., 2011). This first tree was compared according to APG3 to check for misidentification in published sequences. "
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