laduplessis/BESP_paper-analyses

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Created over 5 years ago
Updated over 4 years ago

laduplessis/BESP_paper-analyses

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Bayesian Epoch Sampling Skyline plot (BESP) simulation study and empirical analyses

skylinetools

Utilities and distributions for (birth-death) skyline models.

bdskytools

A package containing several useful R-functions for reading and plotting the results of Birth-Death Skyline (BDSKY) runs in BEAST2.

SARS-CoV-2_Guangdong_genomic_epidemiology

Data used for analyses in "Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China" (Lu et al., Cell, 2020) https://doi.org/10.1016/j.cell.2020.04.023

viroinf-hiddensee

Datasets for the ViroInf Hiddensee workshop

SARS-CoV-2_Northern_California_genomic_surveillance

Data used for analyses in "Genomic Surveillance Reveals Multiple Introductions of SARS-CoV-2 into Northern California" (Deng et al., Science, 2020) https://doi.org/10.1126/science.abb9263

MasterSimulator

Simulate trees in MASTER and test inferences in BEAST2

parameterizedbdsky

Rewrite of bdsky that uses object-orientation to make it easier to extend the model with new parameterizations.

Introduction-to-BEAST2

This is a simple introductory tutorial to help you get started with using BEAST2 and its accomplices.

beast2_bdskysa_ebov_example

Example for BEAST v2.5 paper

beastio

R package with functions for pre- and post-processing of BEAST and BEAST2 files.

CrithidiaGenome

Scripts used to look for signatures of selection in the Crithidia genome using models in codeml

msasummary

Tools for extracting mutations and gaps in multiple sequence alignment and plotting the results

TypeLinkedLocalClock

Beast 2 package which provides a mechanism for linking the rates of a local clock to the types in a MultiTypeTree (http://tgvaughan.github.io/MultiTypeTree) tree structure

besp

The Bayesian Epoch Sampling Skyline Plot

smoothingpriors

This package implements smoothing priors and related utilities for dealing with skyline objects in BEAST2.

BumblebeeImmuneGenes

Scripts used for the paper "A depauperate immune repertoire precedes evolution of sociality in bees" (Barribeau, Sadd, du Plessis and many more), Genome Biology (2015). Scripts may need some debugging for use with different gene sets or organisms. No documentation on the scripts available, please get in touch with me if you have questions.

Treponema_pallidum_in_early_modern_Europe

Data and scripts to reproduce the molecular clock dating analyses presented in "Ancient bacterial genomes reveal a formerly unknown diversity of Treponema pallidum strains in early modern Europe (Majander et al.)