MEGA11: Molecular Evolutionary Genetics Analysis Version 11

Fig. 3.

MEGAs Tree Explorer ( A ) is a feature-rich, versatile viewer of phylogenies

MEGAs Tree Explorer (A) is a feature-rich, versatile viewer of phylogenies that provides many interactive exploration and customization facilities. In MEGA11, the new side toolbar of Tree Explorer makes formatting, rearrangement, and tree exploration tools more accessible and intuitive. Instead of a thin toolbar with nameless buttons, we have opted for a wide toolbar with text labels identifying each tool. The toolbar can be moved to either side of the window, and it can be toggled in and out of view. To organize related tools by groups and accommodate limited vertical space, collapsible panels are used. With the new toolbar, formatting tools previously displayed in external dialogs are readily accessible, and formats are applied instantly instead of after the user closes the external dialog. In addition to the updated toolbar, there are now options for auto-collapsing of nodes containing clusters of taxa belonging to the same group, user-specified cluster size, or by the branch length difference. For very large trees with many similar sequences, this feature can greatly facilitate the visualization of evolutionary events at a glance. An option has been added to export pairwise patristic distances between taxa to a text file for phylogenies and timetrees. For maximum likelihood and maximum parsimony trees where ancestral sequences are present, an option has been added to navigate through sites where a change in the estimated ancestral state differs between the parent and child on the currently selected branch. The tree information box (B) has been updated for timetrees to show branch- and node-specific information, such as earliest and latest sample times in the currently selected subtree, days elapsed between the divergence time for a selected node and the latest sample time, the nearest and furthest tip from a selected node, clade size and clade taxa, and spatiotemporal information if available.

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MEGA11: Molecular Evolutionary Genetics Analysis Version 11