MEGA is an integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence times, mining online databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses. MEGA is used by biologists in a large number of laboratories for reconstructing the evolutionary histories of species and inferring the extent and nature of the selective forces shaping the evolution of genes and species. 
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MEGA-CC provides a command line interface to the computational core in MEGA enabling researchers to automate and pipeline analyses via scripts, other applications, or the built-in file iterator system. - Download PDF
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