CCDpy documentation

This is the documentation for the python implementation of conditional clade distributions (CCDs).

Contents:

• Reading BEAST2 nexus trees
  • _breath_label_nodes()
  • read_nexus_trees()
• Labeling a tree with transmission history
  • _label_all_nodes()
  • _label_all_remaining_unknowns()
  • _label_leaf_and_reachable_nodes()
  • _label_top_infected_nodes()
  • label_transmission_tree()
• Transmission CCDs
  • BaseClade
  • TransmissionAncestryClade
  • TransmissionBlockClade
  • TypeCCD
  • _add_internal_clade()
  • _add_leaf_clade()
  • _build_tree_dict_from_clade_splits()
  • get_transmission_ccd_tree_bottom_up()
  • get_transmission_maps()
  • recursive_nwk_split_dict()
• CLI for transmission CCD-MAP trees