create_starting_tree: Takes an airr clone object and tree and returns BEAST2 XML...

In dowser: B Cell Receptor Phylogenetics Toolkit

Takes an airr clone object and tree and returns BEAST2 XML for setting the starting tree

Description

Takes an airr clone object and tree and returns BEAST2 XML for setting the starting tree

Usage

create_starting_tree(
  clone,
  id,
  tree,
  include_germline_as_tip,
  tree_states,
  start_edge_length
)

Arguments

clone	an airrClone object
id	unique identifer for this analysis
tree	starting tree, either a phylo object or a newick string
include_germline_as_tip	include the germline as a tip
tree_states	use states in the starting tree?
start_edge_length	edge length to use for all branches in starting tree

Value

String of XML setting the starting tree

dowser documentation built on Nov. 5, 2025, 6:36 p.m.