Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting

statistical Statistics (from German: ''Statistik'', "description of a state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a scientific, industria ...

analysis of molecular evolution and for constructing

phylogenetic tree A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

s. It includes many sophisticated methods and tools for

phylogenomics Phylogenomics is the intersection of the fields of evolution and genomics. The term has been used in multiple ways to refer to analysis that involves genome data and evolutionary reconstructions. It is a group of techniques within the larger fields ...

and phylomedicine. It is licensed as proprietary freeware. The project for developing this software was initiated by the leadership of Masatoshi Nei in his laboratory at the

Pennsylvania State University The Pennsylvania State University (Penn State or PSU) is a Public university, public Commonwealth System of Higher Education, state-related Land-grant university, land-grant research university with campuses and facilities throughout Pennsylvan ...

in collaboration with his graduate student Sudhir Kumar and postdoctoral fellow Koichiro Tamura.Kumar, S., K. Tamura, and M. Nei (1993) MEGA: Molecular Evolutionary Genetics Analysis. Ver. 1.0, The Pennsylvania State University, University Park, PA. Nei wrote a monograph (pp. 130) outlining the scope of the software and presenting new statistical methods that were included in MEGA. The entire set of computer programs was written by Kumar and Tamura. The personal computers then lacked the ability to send the monograph and software electronically, so they were delivered by postal mail. From the start, MEGA was intended to be easy-to-use and include solid statistical methods only. MEGA version 2 (MEGA2), which was coauthored by an additional investigator Ingrid Jakobson, was released in 2001.Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei (2001) MEGA2: Molecular Evolutionary Genetics Analysis. Ver. 2.0, Bioinformatics 17:1244-1245. All the computer programs and the readme files of this version could be sent electronically due to advances in computer technology. Around this time, the leadership of the MEGA project was taken over by Kumar (now at Temple University) and Tamura (now at Tokyo Metropolitan University). The monograph ''Molecular Evolutionary Genetics Analysis'' was often used as a textbook for new ways to study molecular evolution. MEGA has been updated and expanded several times and currently all these versions are available from the MEGA website. The latest release, MEGA7, has been optimized for use on 64-bit computing systems. MEGA is in two version. A graphical user interface is available as a native Microsoft Windows program. A command line version, MEGA-Computing Core (MEGA-CC), is available for native cross-platform operation. The method is widely used and cited. With millions of downloads across the releases, MEGA is cited in more than 85,000 papers. The 5th version has been cited over 25,000 times in 4 years.Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 30:2725-2729.

Release history

Features

Sequence alignment construction

*Alignment editor * Multiple sequence alignment *Sequencer (trace) file editor-viewer *Integrated web browser, sequence fetching

Data handling

*Handling ambiguous states: R, Y, T, etc. *Extended MEGA format to save all data attributes *Importing data from other formats: Clustal, Nexus, etc. *Data explorers *Visual specification of domains-groups

Genetic code table section

*Add-edit user defined tables *Compute statistical attributes of a code table *Include all known code tables

Real-time caption expert engine

*Generate captions for distance matrices, phylogenies, tests, alignments *Copy captions to external programs

Integrated text file editor

*Columnar block selection-editing *Line numbers *Utilities to format sequences, reverse complement etc.

Sequence data viewer

*Data export *Highlighting *Statistical quantities estimation

MCL-based estimation of nucleotide substitution patterns

*4x4 rate matrix *Transition-transversion rate ratios: k1, k2 *Transition-transversion rate bias: R

Substitution pattern homogeneity test

*Composition distance *Disparity index *Monte-carlo test

Distance estimation methods

*Nucleotide-by-nucleotide *Synonymous-nonsynonymous:

codon The genetic code is the set of rules used by living cells to translate information encoded within genetic material ( DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links ...

-by-codon *Protein distance *Distance calculations *Sequence diversity calculations *Variance calculations

Tests of selection

*Large sample Z-test *Fisher’s exact test *Tajima’s neutrality test

Molecular clock test

*Tajima’s relative rate test

Tree-making methods

* Neighbor joining *Minimum evolution method * UPGMA * Maximum parsimony * Maximum likelihood *Bootstrap phylogeny test *Confidence probability test *Distance matrix viewer

Tree explorers

*Phylogeny display *Divergence time estimation *Tree editing *Change tree size *Multiple tree display

External links

References

{{Reflist Data visualization software Bioinformatics software