MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

Abstract

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/.

Fig. 1.

The analysis preferences dialog box in MEGA-Proto. It is displayed by the MEGA-Proto application after the user specifies the data type (protein-coding DNA in the present case) and chooses to infer maximum likelihood trees. The user selects the desired settings in this dialog box and saves them into the analysis options file in an appropriate directory for use with MEGA-CC.

Fig. 2.

Steps in using MEGA-Proto and MEGA-CC for iterative analysis.

Fig. 3.

Speed-up achieved in MEGA-CC when inferring ML phylogeny using multiple cores. Each dot shows the time taken by using only one thread divided by the time taken by multiple threads on the same machine. Results are from an analysis using a simulated sequence alignment containing 500 sequences that were 2000 base pairs each (see Tamura et al. 2011). The Subtree-Pruning-and-Regrafting procedure under a GTR + G substitution model (four discrete categories) was used on an Intel Xeon processor with eight hyper-threaded processing cores on Windows 7.