MEGA11

Note: MEGA11 (Molecular Evolutionary Genetics Analysis version 11) is developed by the MEGA team (Sudhir Kumar, Glen Stecher, Koichiro Tamura, and colleagues), not by iGEM. If you meant a different project named MEGA11 from iGEM, please clarify.

MEGA11 is a cross-platform application for building phylogenetic trees and performing comparative analyses of DNA and protein sequences. It integrates sequence alignment, evolutionary model selection, distance calculations, and multiple tree-building methods, including Maximum Likelihood, Neighbor-Joining, Maximum Parsimony, and UPGMA, in an intuitive graphical interface. MEGA11 supports timetree estimation via the RelTime method, codon-based analyses such as dN/dS (nonsynonymous/synonymous substitution rates), ancestral sequence and state reconstruction, bootstrapping, and tests of evolutionary hypotheses. It reads common formats (FASTA, NEXUS, PHYLIP, and MEGA), offers flexible site and codon position filters, and includes rich visualization and annotation tools for trees and distance matrices. In addition to the GUI, a command-line utility (megacc) enables automation and reproducible workflows on Windows, macOS, and Linux. Widely used in evolutionary biology, molecular epidemiology, taxonomy, and comparative genomics, MEGA11 streamlines end-to-end phylogenetic and molecular evolutionary analyses for datasets ranging from small studies to large-scale projects. More