Software

Transtat

An analytic tool (TranStat) is available to analyze data from outbreaks of acute infectious disease to test for the presence of human-to-human transmission (or animal-to-animal in veterinary settings) and to estimate epidemiologic characteristics of the disease.

dms_tools

Software for the analysis and visualization of deep mutational scanning data:
 http://jbloomlab.github.io/dms_tools/  

AbcSmc

Sequential Monte Carlo Approximate Bayesian Computation with Partial Least Squares parameter estimator:
 https://github.com/tjhladish/AbcSmc

pomp:  statistical inference for partially-observed Markov processes

pomp provides a very general realization of nonlinear partially-observed Markov processes (AKA nonlinear stochastic dynamical systems). These are a generalization of linear state-space and hidden Markov models to nonlinear, non-Gaussian processes in either discrete or continuous time. 

http://kingaa.github.io/pomp/

phydms

Software for phylogenetics using deep mutational scanning:
http://jbloomlab.github.io/phydms/

panelPomp

R package for statistical inference on panel partially observed Markov processes (alpha release version).
https://github.com/cbreto/panelPomp

BDAepimodel

Tractable fitting of stochastic epidemic models via Bayesian data augmentation
https://github.com/fintzij/BDAepimodel

phylodyn

Facilitate phylodynamic inference and analysis in an approachable R package.
https://github.com/mdkarcher/phylodyn

unsampled

Estimating unsampled viral diversity
https://github.com/blab/unsampled

lcfit

A specialized surrogate function for phylogenetic likelihoods.
https://github.com/matsengrp/lcfit