KUMAR, S; TAMURA, K; NEI, M; Arizona State Univ., Tempe; Tokyo Metropolitan Univ., Japan; Penn State Univ., University Park: MEGA3: AN INTEGRATED SOFTWARE FOR MOLECULAR EVOLUTIONARY GENETIC ANALYSIS AND SEQUENCE ALIGNMENT

We announce the release of the Molecular Evolutionary Genetics Analysis software version 3.0 (MEGA3) for exploring and analyzing DNA or protein sequences from an evolutionary perspective. MEGA3 provides an intuitive solution for creating, editing, and visualizing sequence alignments using a newly included multiple sequence alignment engine (based on CLUSTALW source code). It has an extensive repertoire of methods for estimating evolutionary distance estimation from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor- joining and maximum parsimony) and two statistical tests of topological differences. Tests for molecular clock as well as substitution/mutation pattern homogeneity among lineages are included. In addition, MEGA3 computes statistical quantities such as nucleotide and amino acid frequencies, transition/transversion biases, codon frequencies (codon usage tables), and the number of variable sites in specified segments in nucleotide and amino acid sequences. MEGA3 also facilitates analyses of large and multigene datasets by providing services for creating groups of sequences and specifying domains and genes. Advanced on-screen sequence data and phylogenetic-tree editors facilitate publication-quality outputs. Integrated and interactive designs, on-line context-sensitive helps, and a text- file editor make MEGA easy to use on the Microsoft Windows platform. MEGA3 can be downloaded free of charge from http://www.megasoftware.net.