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				•

Features

MEGA Version

1.0

2.x

3.x

4.x

Platform

DOS

Win

Win

Win