Hi, community members
Is there any general idea about how to set the parameters for the interpretation of LBI?
How to evaluate these 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]
Calculate LBI for a given tree and one or more sets of parameters.
optional arguments:
-h, --help show this help message and exit
--tree TREE Newick tree (default: None)
--branch-lengths BRANCH_LENGTHS
JSON with branch lengths and internal node dates
estimated by TreeTime (default: None)
--output OUTPUT JSON file with calculated distances stored by node
name and attribute name (default: None)
--attribute-names ATTRIBUTE_NAMES [ATTRIBUTE_NAMES ...]
names to store distances associated with the
corresponding masks (default: None)
--tau TAU [TAU ...] tau value(s) defining the neighborhood of each clade
(default: None)
--window WINDOW [WINDOW ...]
time window(s) to calculate LBI across (default: None)
--no-normalization disable normalization of LBI by the maximum value
(default: False)
Best wishes,
Yang