Computational diagnosis of amino acid variants in the human exome is the first step in assessing the disruptive impacts of non-synonymous single nucleotide variants (nsSNVs) on human health and disease. The Molecular Evolutionary Genetics Analysis software with mutational diagnosis (MEGA-MD) is a suite of tools developed to forecast the deleteriousness of nsSNVs using multiple methods and to explore nsSNVs in the context of the variability permitted in the long-term evolution of the affected position. In its graphical interface for use on desktops, it enables interactive computational diagnosis and evolutionary exploration of nsSNVs. As a web service, MEGA-MD is suitable for diagnosing variants on an exome scale. The MEGA-MD suite intends to serve the needs for conducting low- and high-throughput analysis of nsSNVs in diverse applications.

UNLABELLED: There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows. Therefore, we now make available the computing core of the MEGA software as a stand-alone executable (MEGA-CC), along with an analysis prototyper (MEGA-Proto). MEGA-CC provides users with 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. Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis. AVAILABILITY: http://www.megasoftware.net/.