MEGA, Molecular Evolutionary Genetics Analysis
|
Version 5 (2011) | |
| Original author(s) | Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, Sudhir Kumar |
|---|---|
| Stable release | v6.06 |
| Operating system | Microsoft Windows, Mac OS X |
| Type | Bioinformatics |
| License | Freeware |
| Website |
www |
MEGA, Molecular Evolutionary Genetics Analysis, is a freely available software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. The project for developing this software was initiated by the leadership of Masatoshi Nei in his laboratory at the Pennsylvania State University in collaboration with his graduate student Sudhir Kumar and postdoctoral fellow Koichiro Tamura.[1] Nei wrote a monograph (pp. 130) outlining the scope of the software and presenting new statistical methods that were included in MEGA. However, the entire set of computer programs was written by Kumar and Tamura. Because the personal computers at that time did not have the capability of sending the monograph and the software electronically, they were delivered by postal mail. From the beginning, MEGA was intended to be an easy-to-use software and include solid statistical methods only.
MEGA version 2 (MEGA2), which was coauthored by an additional investigator Ingrid Jakobson, was released in 2001.[2] All the computer programs and the readme files of this version could be sent electronically because of the advancement of computer technology. Around this time, the leadership of the MEGA project was taken over by Kumar (now at Arizona State University) and Tamura (now at Tokyo Metropolitan University). Despite this humble start, MEGA1.[1] has been cited at least 2,493 times according to ISI. The monograph “Molecular Evolutionary Genetics Analysis” was often used as a textbook for new ways of studying molecular evolution.
MEGA has been updated and expanded several times (release history), and currently all these versions are available from the MEGA home page (www
Release History
| Version | Release Date |
|---|---|
| 1.0 | 1993 [1] |
| 1.1 | 1994 [4] |
| 2.0 | 2000 [2] |
| 2.1 | 2001 [2] |
| 3.0 | 2004 [5] |
| 4.0 | 2006 [6] |
| 4.1 | 2008 [6] |
| 5.0 | 2011 [7] |
| 5.1 | Oct 2012 [7] |
| 5.2 | April 2013 [7] |
| 6.0 | December 2013 [8] |
Features
Sequence Alignment Construction
- Alignment Editor
- Multiple Sequence Alignment
- Sequencer (Trace) File Editor/Viewer
- Integrated Web Browser and 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
- Computation of Statistical Attributes of a Code Table
- Inclusion of 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-by-Codon)
- Protein Distance
- Distance Calculations
- Sequence Diversity Calculations
- Variance Calculations
Tests of Selection
- Large Sample Z-Test
- Fisher’s Exact Test
- Tajima’s Test of Neutrality
Molecular Clock Test
- Tajima’s Relative Rate Test
Tree-Making Methods
- Neighbor-Joining
- Minimum Evolution Method
- UPGMA
- Maximum Parsimony
- Bootstrap Test of Phylogeny
- Confidence Probability Test
- Distance Matrix Viewer
Tree Explorers
- Phylogeny Display
- Divergence Time Estimation
- Tree Editing
- Change Tree Size
- Multiple Tree Display
External links
- MEGA, a freely available software
- MEGA website for Japanese users
- MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. (2008) Kumar S, Dudley J, Nei M & Tamura K. Briefings in Bioinformatics Vol.9, pages 299-306 weblink.
References
- ↑ 1.0 1.1 1.2 Kumar, S., K. Tamura, and M. Nei (1993) MEGA: Molecular Evolutionary Genetics Analysis. Ver. 1.0, The Pennsylvania State University, University Park, PA.
- ↑ 2.0 2.1 2.2 Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei (2001) MEGA2 : Molecular Evolutionary Genetics Analysis. Ver. 2.0, Bioinformatics 17:1244-1245.
- ↑ "MEGA Update History". MEGA: Molecular Evolutionary Genetics Analysis. Retrieved 20 June 2013.
- ↑ Kumar, S., K. Tamura, and M. Nei (1994) MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers. CABIOS 10:189-191.
- ↑ Kumar, S., Tamura, K., and Nei, M. (2004) MEGA3: Molecular Evolutionary Genetics Analysis. Brief. Bioinformatics 5:150-163.
- ↑ 6.0 6.1 Tamura, K., Dudley, J., Nei, M., Kumar, S. (2007) MEGA4 : Molecular Evolutionary Genetics Analysis. Mol. Biol. Evol. 24(8):1596-1599.
- ↑ 7.0 7.1 7.2 Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. (2011) MEGA5 : Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 28:2731-2739.
- ↑ 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.