This repository holds the data, code, and manuscript for the project by Sarah Hilton and Jesse Bloom that analyzes the effect of using models with site-specific stationary states on the estimation of deep branches. Specifically, this project looks at the difference between GY94 models and ExpCM's on the estimation of branch lengths on an influenza HA phylogenetic tree.
The manuscript is titled "Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral divergence."
A pre-print describing this study is available on bioRxiv at DOI 10.1101/302703.
This repo contains the following directories:
./manuscript/: contains the manuscript describing the project.
./analysis/: contains the code and analysis for the project.