process about local branching index (LBI) analysis

[virologist]

Hi, @rneher

Very interesting tool about fitness inference.
Is there anything like wiki or analysis protocol to follow to execute the LBI analysis?
I feel confused with parameter setting.

%%bash
infer_fitness.py \
--aln aligned.fas \
--outgroup EPI123456 \
--eps_branch 10e6 \
--tau 0.25 \  #???
--gamma 1 \
--omega \  #???
--collapse \ #???
--plot 

I also find the Nextstrain is able to analyze the LBI. Again, I don't have the sense to set the parameters.
Any help will be greatly appreciate.

Beast wishes,
Yang