MEGA

The software provides an integrated environment for analyzing DNA and protein sequences, supporting both automatic and manual alignment, phylogenetic tree inference, and evolutionary hypothesis testing. It offers tools for mining web‑based databases, estimating molecular evolution rates, and performing statistical methods such as maximum likelihood, distance, ordinary least squares, maximum parsimony, composite likelihood, and Bayesian analyses. Recent versions include a fast, filtered substitution model selection that skips sub‑optimal models, an adaptive bootstrap for maximum likelihood searches, and the DrPhylo module for assessing clade stability.

Target users are researchers and students working in molecular evolution, phylogenetics, and related biological fields who need a graphical or command‑line interface for sequence analysis and tree construction. The suite runs on macOS (core platform) and includes additional platforms, with both 64‑bit and 32‑bit builds available.

Distinctive aspects include a redesigned Tree Explorer toolbar, a Calibration Editor linked to the TimeTree database for time estimates, and an AI‑powered assistant (MEGA‑GPT) that helps users navigate the software. Instructional videos and extensive documentation support learning and application of the tool’s many visual and analytical features.