augur lbi

Calculate LBI for a given tree and one or more sets of parameters.

usage: augur lbi [-h] --tree TREE --branch-lengths BRANCH_LENGTHS --output
                 OUTPUT --attribute-names ATTRIBUTE_NAMES
                 [ATTRIBUTE_NAMES ...] --tau TAU [TAU ...] --window WINDOW
                 [WINDOW ...] [--no-normalization]

Named Arguments

--tree

Newick tree

--branch-lengths

JSON with branch lengths and internal node dates estimated by TreeTime

--output

JSON file with calculated distances stored by node name and attribute name

--attribute-names

names to store distances associated with the corresponding masks

--tau

tau value(s) defining the neighborhood of each clade

--window

time window(s) to calculate LBI across

--no-normalization

disable normalization of LBI by the maximum value

Default: False