Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

Source code

github.com/blab/flu-forecasting

Contributors

huddlej

trvrb

rneher

Latest commits

15 Oct 2020 - Merge pull request #2 from blab/blog-post Add blog post content

15 Oct 2020 - Update blog post html

07 Oct 2020 - Finished table with classes to highlight status

07 Oct 2020 - Clean up references in blog post Use the "et al." abbreviation when there are more than two authors (note custom CSL for pandoc-citeproc and updated pandoc command in the README), added citations for simulation software, and added URLs to all references.

06 Oct 2020 - Finished complete draft of blog post Adds section comparing our two studies and refines the conclusion section.

Pages

/ data / simulations /

/ analyses / projected-frequencies /

/ analyses / identify-optimal-lbi-parameters /

/ manuscript / blog-post /

Simulated HA sequences

The sequences in this directory represent 90 years of flu HA simulations (1000 bases). The first 200 sites (modulo 3) are "epitope" sites. Richard Neher added functionality to FFPopSim to handle reassortment (that is a defined recombination break point between segments). Modification of default parameters produces roughly flu-like trees. Note that FFPopSim assumes a binary alphabet.