Command reference

PhyKIT commands are organized below by analytical task. Each command has one canonical page containing its identity, live runtime interface, scientific guidance, output interpretation, examples, limitations, validation, and citations.

Choose by task

• Alignment & dataset utilities (9 commands)

• Alignment quality & statistics (20 commands)

• Evolutionary rate analysis (3 commands)

• Homology assessment (3 commands)

• Introgression & gene flow (4 commands)

• Other utilities (1 commands)

• Phylogenetic comparative methods (8 commands)

• Phylogenetic signal (3 commands)

• Saturation & model adequacy (2 commands)

• Trait evolution (20 commands)

• Tree comparison & consensus (12 commands)

• Tree manipulation & utilities (14 commands)

• Tree summary statistics (13 commands)

All commands

Use the machine-readable command catalog for programmatic discovery of commands, aliases, arguments, and documentation URLs.