Molecular Evolutionary Genetics Analysis: Difference between revisions
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Revision as of 14:03, 7 September 2013
| File:MEGA Molecular Software Logo.png | |
| Original author(s) | Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, Sudhir Kumar |
|---|---|
| Stable release | v5.2.2
|
| Operating system | Microsoft Windows, Mac OS X |
| Type | Bioinformatics |
| License | Freeware |
| Website | www |
MEGA, Molecular Evolutionary Genetics Analysis, is a freely available software to aid scientists and academia in making phylogenetic trees using nucleotide or protein sequences. It is developed by Koichiro Tamura from Tokyo Metropolitan University, Daniel Peterson, Nicholas Peterson, Glen Stecher, Sudhir Kumar from Arizona State University, and Masatoshi Nei from Pennsylvania State University. The manuscripts describing this resource are among the most highly cited in biology.[1][2][3][4][5]
Currently, MEGA is available in its regular version 5.2.2 and previous versions (4.02, 3.1, DOS) from its homepage.
Release History
| Version | Release Date |
|---|---|
| 1.0 | 1993 |
| 1.1 | 1994 |
| 2.0 | 2000 |
| 2.1 | 2001 |
| 3.0 | 2004 |
| 4.0 | 2006 |
| 4.1 | 2008 |
| 5.0 | 2011 |
| 5.1 | Oct 2012 |
| 5.2 | April 2013 |
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 (Clusal/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
- ^ Kumar S, Tamura K, Nei M (1994). "MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers". Comput. Appl. Biosci. 10 (2): 189–91. PMID 8019868.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Kumar S, Tamura K, Jakobsen IB, Nei M (2001). "MEGA2: molecular evolutionary genetics analysis software". Bioinformatics. 17 (12): 1244–5. doi:10.1093/bioinformatics/17.12.1244. PMID 11751241.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Kumar S, Tamura K, Nei M (2004). "MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment". Brief. Bioinformatics. 5 (2): 150–63. PMID 15260895.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ Tamura K, Dudley J, Nei M, Kumar S (2007). "MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0". Mol. Biol. Evol. 24 (8): 1596–9. doi:10.1093/molbev/msm092. PMID 17488738.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ 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 (10): 2731–9. doi:10.1093/molbev/msr121. PMID 21546353.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ "MEGA Update History". MEGA: Molecular Evolutionary Genetics Analysis. Retrieved 20 June 2013.