reptalex

phylofactor

SARS2_Reverse_Genetics

phylogenomic analysis of restriction sites & reverse genetic systems

covid_r_v_D

EarlyWuhan

Early outbreak medical alerts & contact tracing biases

NYC_BA2_dashboard

Dashboard of short-term forecasts for the New York City BA.2 outbreak

BBS

Code for BBS fluctuation analysis

BirdPhylofactor

Models for phylofactoring bird data

COVID_ERL

Analysis of epidemic resistance lines and endpoints for COVID epidemics

COVID_fast_v_slow

Script for the analysis of COVID confirmed count data & testing fast vs. slow epidemic hyotheses

dendromap

Mapping time-scaled reference trees to microbial phylogenies

Generalized-Phylofactorization-Scripts-and-Workspaces

Scripts and Workspaces to replicate analyses in "Phylofactorization: a graph partitioning algorithm to identify phylogenetic scales in ecological data"

PercolationSpillover

Code for simulation and analysis of spillover count datasets

phylodt

metapopulation phylodynamic simulations with cross reactivity

phylogenetic-tutorials

q2-phylofactor

voc_outbreak_time

Common duration SARS-CoV-2 outbreaks caused by VOCs

WrightFisher

R package for simulation and CVT-testing of Wright-Fisher Process