Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, and Sudhir Kumar (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Likelihood, Distance, and Parsimony methods. Molecular Biology and Evolution.
(to be submitted)
Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.
- Download PDF
Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
- Download PDF

 

 

Features

All features are listed in the table below.

MEGA Version
1.0
2.x
3.x
4.x
Platform
DOS
Win
Win
Win

Input Data

DNA, Protein, Pairwise distance matrix

Sequence Alignment Construction

Alignment Editor

      Manual editing of DNA and Protein sequences

 

 

      Motif searching/highlighting

 

 

      Synchronous alignment editing of original and translated cDNA

 

 

      Copy/Paste sequences To/From Clipboard

 

 

      Save alignment session for future display

 

 

      Ability to read sequencer, MEGA, NEXUS, FASTA, and other formats

 

 

      Apply color/highlight schemes to sequence data

 

 

      Write alignment to MEGA file for direct analysis in MEGA

 

 

      BLAST sequences from alignment directly

 

 

Multiple Sequence Alignment

      Complete native implementation of ClustalW

 

 

      Ability to select all options on the fly

 

 

      Ability to align any user-selected region

 

 

      Ability to align translated cDNA sequences and automatic adjustment

 

 

Sequencer (Trace) File editor/viewer

      View ABI (*.abi, .ab1) and Studfen (*.std?)

 

 

      Edit trace file

 

 

      Mask vector (or any other region)

 

 

      Launch direct BLAST search for whole or selected sequence

 

 

      Send data directly to Alignment Editor

 

 

Integrated Web Browser and Sequence Fetching

      Direct "usual" web and GenBank browsing from MEGA

 

 

      One-click sequence fetching from databanks queries

 

 

      Send sequence data from BLAST search directly into alignment

 

 

      Bookmark favorite sequence databank sites

 

 

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

      Sequence

      Distance matrix

 

Attributes supported

      Groups of Sequences/Taxa

 

      Domains

      Genes and Mixed Domain attributes

 

      Explicit labels for sites

 

      Automatic codon translation

      Selection of codon positions

      Selection of different site categories

 

Visual Specification of Domains/Groups

 

Center Analysis Preferences Dialog

 

 

Unlimited Data size for Analysis

 

Genetic Code Table Selection

Choose a desired table

Ability to add/edit user defined tables

 

Computation of statistical attributes of a code table

      Degeneracy of codon positions

 

      Numbers of potential synonymous sites

 

Inclusion of all known code tables

 

Real-Time Caption Expert Engine

Generate Captions for Distance Matrices

 

 

 

Generate Captions for Phylogenies

 

 

 

Generate Captions for Tests

 

 

 

Generate Captions for Alignments

 

 

 

Copy Captions to External Programs

 

 

 

Save/Print Captions

 

 

 

Integrated Text File Editor

Unlimited Text File Size

 

Multi-file Tabbed Display

 

Columnar Block selection/Editing

 

Undo/Redo operations

 

Line numbers

 

Utilities to Format Sequences/Reverse complement etc.

 

Copy Screenshots to EMF/WMF/Bitmap for presentation

 

Sequence Data Viewer

Two dimensional display of molecular sequences

Display with identity symbol

 

Drag-drop sorting of sequences

 

Mixing coding and non-coding sequence display

 

One-click translation

Display with all or only selected taxa

 

Data Export

      PAUP3, PHYLIP

      PAUP4, PHYLIP Interleaved

 

Highlighting

      0,2,4-fold degenerate sites

Variable, parsimony informative sites

      Constant Sites

 

Statistical Quantities estimation

DNA and protein sequence compositions

Estimation by genes/domains/groups

 

                Codon Usage

Estimation by genes/domains/groups

 

                Use only highlighted sites

 

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

   Models

      No. of differences, p-distance, Jukes-Cantor, Kimura 2P

      Tajima-Nei, Tamura 3-parameter, Tamura-Nei distance

      LogDet (Tamura-Kumar)

     

     

      Maximum Composite Likelihood

 

 

 

    Subcomponents

      Transitions (ts), tranversions (tv), ts/tv ratio

      Number of common sites

 

    Account for rate variation among sites

    Relaxation of the homogeneity assumption

 

 

Synonymous/Nonsynonymous (Codon-by-Codon)

    Models

      Nei-Gojobori (1986) method

      Modified Nei-Gojobori method

 

      Li-Wu-Lou, PBL, Kumar method

 

    Subcomponents

      Synonymous (s), nonsynonymous (n) distances

      Numbers of synonymous and nonsynonymous sites

 

      Differences and ratios (s-n, n-s, s/n, n/s)

 

      4-fold degenerate site distances

 

      0-fold degenerate site distances

 

      Number of 0-fold and 4-fold degenerate sites

 

Protein distance

      Number of differences, p-distance, Poisson

      Dayhoff and JTT distances

 

 

      Account for rate variation among sites

 

      Relaxation of the homogeneity assumption

 

 

Distance Calculations

      Pairwise

      Between Group Average

     

      Within Group Average

 

      Net between group Average

 

      Overall average

 

Sequence Diversity Calculations

      Mean Diversity within Subpopulations

 

      Mean Diversity for Entire Populaton

 

      Mean Interpopulational Diversity

 

      Coefficient of Differentiation

 

Variance Calculations

      Analytical

      Bootstrap

 

Handling missing data

Automatic translation

Automatic pasting of partial codons between exons

 

Tests of Selection

Codon-based tests

      Large sample Z-test

                Between Sequences

                Within groups

 

                Overall sequences

 

      Fisher's Exact Test

 

Tajima's Test of Neutrality

 

Molecular Clock Test

Tajima's relative rate test

 

Tree-making Methods

Neighbor-Joining

      Randomized tie-breaking in bootstrapping

 

Minimum Evolution method

 

      Branch-swapping (Close-Neighbor-Interchange; CNI)

 

      Fast OLS computation method

 

UPGMA

      Randomized tie-breaking in bootstrapping

 

Maximum Parsimony

      Nucleotide sequences

      Protein sequences

 

      Max-mini branch-and-bound and min-mini searches

      Branch-swapping (CNI)

 

      Average branch length estimation

 

Bootstrap Test of Phylogeny

      Neighbor-joining/UPGMA

      Minimum Evolution

 

      Maximum Parsimony

 

Confidence Probability Test

      Neighbor-joining

      Minimum Evolution

 

Consensus tree construction

Condensed tree construction

Distance Matrix Viewer

View pairwise distances

 

View between group distances

 

View within group distances

 

View distances and standard errors simultaneously

 

Sort the distance matrix

 

      Drag-and-drop

 

      Group-wise

 

      By Sequence names

 

Control display precision

 

Export Data for printing or re-importing

 

Tree Explorers

Phylogeny Display and Graphic printing

On-the-spot taxa name editing

 

Multiple phylogeny views

 

Linearized Tree

 

Estimation of divergence time by calibrating molecular clock

 

Copy to Clipboard/save to file as an EMF drawing

 

Save to Newick format

 

 

Read trees from Newick format

 

 

User specified control for

      Placement and precision of branch length

 

      Scale bar addition

 

      Collapsing branches or groups

 

      Display only a subtree

 

      Ability to view multiple trees in different viewers

 

Tree Editing

      Flipping, re-rooting

 

      Add marker symbols to names

 

      Multi-color display and printing

 

Change Tree Size

      Vertical separation between taxa

 

      Horizontal size

 

      Change Tree shape

 

Multiple tree display

 

Save tree session for future display

 

What you see is what you get printing

 

Multi- or single page printing

 

Display images on tree for groups and taxa

 

 

Other Features

Multi-user and multi-threading support

 

 

 

Linux version