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


Newick tree


JSON with branch lengths and internal node dates estimated by TreeTime


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


names to store distances associated with the corresponding masks


tau value(s) defining the neighborhood of each clade


time window(s) to calculate LBI across


disable normalization of LBI by the maximum value

Default: False