Version 6 contains a number of enhancements over MEGA 5. They include
Added a Time Tree system for estimating relative and absolute times of divergence for all branching points in a phylogeny that is based on the Reltime method described in Tamura et al. 2012 and which supports multiple user-defined calibration constraints.
Added a mutation diagnosis system for exploring the functional impact of non-synonymous single nucleotide variants (nSNVs) that uses the EvoD server. This system is based on the evolutionary diagnosis method described in Kumar et al. 2012.
MEGAs capacity to allocate system memory has been doubled for 64-bit computers by setting the IMAGE_FILE_LARGE_ADDRESS_AWARE bit.
The Tree Explorer was enhanced to allow for the display of trees with up to ~4,000 taxa.
A birds eye summary view was added to the Sequence Data Explorer. This view facilitates fast navigation across genes and domains.
The LG amino acid model (Le and Gascuel 2008) was added for amino acid and protein-coding data.
For Maximum Parsimony phylogeny construction, the CNI search method was replaced by the Subtree-Pruning-Regrafting (SPR) and the Tree-Bisection-Reconnection (TBR) approaches.
Added support for internal node labels in Newick files (a node label at the root is not supported). Internal node labels should be placed in single quotes.
Added a utility for displaying node ids in the Tree Explorer (click View | Show/Hide | Node Ids)
Support for groups was added to the Alignment Explorer.
Added support for exporting to fasta files from the Sequence Data Explorer.