Using DeltaBS and random forests to detect niche adaptation

Here, we outline an approach to identifying patterns of increased mutational burden in genes associated with a phenotype.

This repository should allow you to do two things:

• Build you own model for learning which genes are involved in adaptation to the niche or phenotype you are studying
• Use our model of Salmonella invasiveness to determine the invasiveness index of your own Salmonella isolates.

It also contains the code used to perform the analysis in the manuscript which accompanies this approach.

Requirements

To run these analyses, you need to have Perl, R, R Studio and HMMER3.0 installed, and will need to install some R packages, outlined in each of the R notebooks provided for analysis.