Request: a script to figure out input parameters

[lskatz]

This is kind of a long-term request since it is so difficult but probably very useful. I feel like it is possible to estimate many of the parameters in the config file.

Many of these parameters could be estimated from the original data using, I believe, ClonalFrameML on the genome assemblies, standard read metrics from the original fastq files, and a profile that ART generates.

This would be a separate script but I think worth having in the TTR package long-term.

[snacktavish]

I'll think about it... I think that I want researchers to dig into aspects of the evolutionary model themselves, in order to really get a feel for what is affecting their phylogenetic analyses. It would be possible to set up scripts to complete the full loop from reads to evolutionary model, to tree, to simulations, to reads, to tree, but I worry it would be too black box. Anyhow - I'll consider it!