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