MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses. MEGA is a multi-threaded Windows application. It runs on all releases of Microsoft Windows operating system... (
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The program works with the following extensions: 
mts, 
mas, 
fas, 
fsa, 
tre, 
meg, 
nwk and 
fasta