treetime.rst

TreeTime class documentation

TreeTime is the top-level wrapper class of the time tree inference package. In addition to inferring time trees, TreeTime can reroot your tree, resolve polytomies, mark tips that violate the molecular clock, or infer coalescent models. The core time tree inference is implemented in the class ClockTree.

TreeTime docstring and constructor

treetime.TreeTime

Main pipeline method

treetime.TreeTime.run

Additional functionality

treetime.TreeTime.resolve_polytomies

treetime.TreeTime.relaxed_clock

treetime.TreeTime.clock_filter

treetime.TreeTime.reroot

treetime.TreeTime.plot_root_to_tip

treetime.TreeTime.print_lh

treetime.plot_vs_years