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bdmm-cascade

BEAST 2 package for fitting multi-type birth-death models to phylogenies conditional on mapped types.

bdmm-prime

Modified implementation of the BDMM multi-type birth-death model for BEAST 2.

deeptswvseq

Python scipts used to analyze TSWV deep sequence data.

emsi-sars-cov-2

EMSI SARS-CoV-2 Phylodynamics Team Project

espalier

Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests.

git-example

Just an example repo for demonstration

git-lab-story

A story example

jphylter0.1

Phylodynamic inference for stochastic epidemiological models using particle filtering.

lumiere

BEAST 2 package for phylodynamics with adaptive molecular evolution using the Marginal Fitness Birth-Death model

marula

A BEAST 2 package for phylodynamic inference using epidemiological models with multiple (nested) forms of population structure and time-varying parameters.

molepi

mutantigen

Phylodynamic simulations of influenza virus evolution with antigenic and deleterious mutations, implented in Java. This is a modified version of Trevor Bedford's program Antigen (http://bedford.io/projects/antigen/). For more information on the model, see: http://dx.doi.org/10.7554/eLife.07361

pairtree

Phylodynamic network analysis using pairwise epidemic and coalescent models implemented in BEAST 2.

phylo-particlemcmc

Phylodynamic inference using particle filtering and particle MCMC. Implemented in Matlab. See Rasmussen et al. (2011) for a full description of the algorithms: https://doi.org/10.1371/journal.pcbi.1002136

phylotf2

Efficient likelihood-based phylodynamic learning using birth-death models in TensorFlow.

pleiotropymetaanalysis

Data from our meta-analysis of pleiotropic fitness effects of viral mutations

recbreakdetect

Simulation code and data for localizing recombination breakpoints in sequence data.

rtd-tutorial

Test for hosting project docs on Read the Docs

sir-binder

Jupyter notebooks for SIR epidemic models hosted on binder.

squamish-beast-tamers-2023-lectures

Repository for lectures held at the 2023 TTB workshop in Squamish, British Columbia.

virusesacrosstreeoflife

Slide deck introducing high school students to the diversity of viruses infecting bacteria, plants and invertebrates.