Mega2 is a data manipulation software for applied statistical genetics. Mega is an acronym for Manipulation Environment for Genetic Analysis. The software allows the applied statistical geneticist to convert one's data from several input formats to a large number output formats suitable for analysis by commonly used software packages. In a typical human genetics study, the analyst often needs to use a variety of different software programs to analyze the data, and these programs usually require that the data be formatted to their precise input specifications. Conversion of one's data into these multiple different formats can be tedious, time-consuming, and error-prone. Mega2, by providing validated conversion pipelines, can accelerate the analyses while reducing errors. Mega2 produces a common intermediate data representation using SQLite3, which enables the data to be accessed by other programs and languages. In particular, th
Mega2R
R package converts the SQLite3 data into R data frames. Several R functions are provided that illustrate how data can be extracted from the data frames for common R analysis, such a
SKAT
an
pedgene
The key is being able to efficiently extract genotypes corresponding to chosen subsets of markers so as to facilitate gene-based association testing by automating looping over genes in the genome. Another function converts to VCF format and another converts the data t
GenABEL
format. For more information about the Mega2R package, se
here
Mega2 has been used to facilitate genetic analyses of a wide variety of human traits, including hereditary dystonia, Ehlers-Danlos syndrome, multiple sclerosis, and gliomas. A list of PubMed Central articles citing Mega2 can be see
here
Mega2, which focusses on data reformatting, should not be confused with the

MEGA, Molecular Evolutionary Genetics Analysis Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. It includes many sophisticated methods and tools for phylogenomics and phy ...

program, which focuses on molecular evolution and phylogenetics.

Input file formats

Mega2 accepts input data in a variety of widely used file formats. These contain, at a minimum, data about the phenotypes, the marker genotypes, any family structures, and map positions of the markers.

Output file formats

Mega2 supports conversion to the following output formats.

Documentation

The Mega2 documentation is availabl
here
in HTML format, an
here
in PDF format.

References

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External links

Download Mega2

Mega2 documentation (PDF)

Mega2 users Google Group

Mega2 bitbucket repository

The Mega2R R package
Free bioinformatics software