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.
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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.
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All features are listed in the table below.

MEGA Version

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


      Distance matrix


Attributes supported

      Groups of Sequences/Taxa



      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


      PAUP4, PHYLIP Interleaved



      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



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

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

      LogDet (Tamura-Kumar)



      Maximum Composite Likelihood





      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)


      Nei-Gojobori (1986) method

      Modified Nei-Gojobori method


      Li-Wu-Lou, PBL, Kumar method



      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


      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




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


      Randomized tie-breaking in bootstrapping


Minimum Evolution method


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


      Fast OLS computation method



      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


      Minimum Evolution


      Maximum Parsimony


Confidence Probability Test


      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






      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