This document describes MEGA4 software features for DNA sequence editing, alignment, evolutionary distance estimation, and phylogenetic tree inference.
MEGA4 is a software tool designed for molecular evolutionary genetics analysis. It provides facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, and analyzing sequence alignments to estimate evolutionary distances. The software also supports inferring phylogenetic trees and testing evolutionary hypotheses. Version 4.0 is a native 32-bit Windows application with multi-threading and multi-user support, and it is available free of charge.
MEGA4 is a native 32-bit Windows application and can also run on Linux desktop environments via the Wine compatibility layer and on Intel-based Macintosh computers under the Parallels program.
MEGA4 includes a Caption Expert software module that generates descriptions for every result obtained by the software in figure legend format.
MEGA4 implements the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously.