Download MEGA Computing Core:
http://www.megasoftware.net/megaccusage.php

There is a growing need to apply MEGA's capabilities for batch processing large datasets and for integrative analysis purposes. MEGA-CC provides the MEGA computing core as a stand-alone executable, along with an analysis prototyper (MEGA-Proto). It gives access to all the computational analyses available through MEGA's graphical user interface version. This includes methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference. Additionally, we have upgraded the source code for phylogenetic analysis using the maximum likelihood methods for parallel execution on multiple processors and cores.