Molecular Evolutionary Genetics Analysis

BioCodeKb - Bioinformatics Knowledgebase

MEGA is desktop computer application used for comparative analysis of homologous gene sequences either from multigene families or from different species with a special attention on gathering evolutionary relationships and patterns of DNA and protein evolution for managing statistical analysis of molecular evolution and for constructing phylogenetic trees of these sequences. It includes many advanced methods and tools for phylogenomics and phylomedicine with a graphical user interface. It is licensed as patently freeware. It allows the researchers in viewing and editing of the aligned input sequence data and gives many tools for phylogenetic and statistical analysis of the alignments and gives results in the form of interactive phylogenetic trees and evolutionary distance matrices.


The repository in MEGA includes features focusing to determine gene duplication events in gene family trees. Moreover, this tool is available through a graphical user interface (GUI) and a command line interface.


MEGA evolves time to time to help researchers in their growing need to analyze large dataset using new computational methods.


Phylogenetic trees show hypotheses about the evolutionary relationships among a group of organisms. The sequences of genes or proteins can be compared among species and used to build phylogenetic trees. Typically few sequence differences represents the closely related species, while less related species shows more differences in their sequence.


It uses the Neighbor joining Method, UPGMA, Me and Mp algorithms to develop the phylogenetic trees.


Features of MEGA tool

  • Sequence alignment construction

  • Data handling

  • Genetic code table section

  • Real-time caption expert engine

  • Integrated text file editor

  • Sequence data viewer

  • MCL-based estimation of nucleotide substitution patterns

  • Substitution pattern homogeneity test

  • Distance estimation methods

  • Tests of selection

  • Molecular clock test

  • Tree-making methods

  • Tree explorers

  • Real-Time Caption Expert Engine

  • Multi-User and Multi-Threading Support


Uses of MEGA

  • Classifying the sequence data

  • Finding unique regions

  • Comparison of sequence data with a global data set

  • Identification of new genes and proteins

  • Estimate the rate of molecular evolution

  • Examining the phylogeny of antibiotic resistance genes

  • Selection confirmation

  • Evolutionary distance measurements

  • Phylogenetic tree evaluation

  • Genes/Domains identification

  • Highest number of citations

  • No codes to memorize

  • Flexible

  • Combines the functions of Clutal Omega, PAUP,BIODIT and TREEDIST

  • Perform evolutionary tests

Download data from database,/file/sequencer


Retrieve the sequence from database, data bank or BLAST search to build sequence alignments. By selecting ADD TO ALIGNMENT option, MEGA exports the sequences automatically to the alignment explorer for producing multiple sequence alignments. Alignment explorer provides two approaches using ClustalW through which data could be displayed as DNA sequence and translated amino acid. Our results show the bootstrap values, evolutionary parameters, molecular clock etc.


MEGA runs a statistical re-sampling process called bootstrapping to check trees reliability by measuring the probability of branch recovery if the taxa were sampled again. Its values are typically from 1000 repeated calculations and values >70% is acceptable.


The results are shown in many ways such as topologies without branch length e.g. Cladogram or with estimated branch length e.g. Phylogram or in linearized fashioned by means of tree explorer.

open a saved alignment session and click on the Data menu. Select the Export alignment into MEGA format. Click 'NO' when asked if your sequence data encodes for protein. This file will have a .

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