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Abstract
With its theoretical basis firmly established in molecular evolutionary and population
genetics, the comparative DNA and protein sequence analysis plays a central role in
reconstructing the evolutionary histories of species and multigene families, estimating
rates of molecular evolution, and inferring the nature and extent of selective forces
shaping the evolution of genes and genomes. The scope of these investigations has
now expanded greatly owing to the development of high-throughput sequencing techniques
and novel statistical and computational methods. These methods require easy-to-use
computer programs. One such effort has been to produce Molecular Evolutionary Genetics
Analysis (MEGA) software, with its focus on facilitating the exploration and analysis
of the DNA and protein sequence variation from an evolutionary perspective. Currently
in its third major release, MEGA3 contains facilities for automatic and manual sequence
alignment, web-based mining of databases, inference of the phylogenetic trees, estimation
of evolutionary distances and testing evolutionary hypotheses. This paper provides
an overview of the statistical methods, computational tools, and visual exploration
modules for data input and the results obtainable in MEGA.