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bdsky

Birth Death Serial Skyline Model for BEAST2

bdskytools

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

beast2

Bayesian Evolutionary Analysis by Sampling Trees

beast2-unreleased-packages

Backup repository for unreleased BEAST2 packages

beast2_bdskysa_ebov_example

Example for BEAST v2.5 paper

beast2_template

A simple Python script to create BEAST2 XML files from templates

beastio

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

besp

The Bayesian Epoch Sampling Skyline Plot

besp_paper-analyses

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

blotter

bedford lab research

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.

chcoviddashboard

Covid-19 Dashboard for Switzerland

clads-tutorial

Tutorial on the ClaDS package for the Taming the BEAST website

crithidiagenome

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

grapevine

Process consensus file for COG-UK data

introduction-to-beast2

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

jekylltest

Test default Jekyll website

laduplessis.github.io

likelihoodsurface

Grid points on the likelihood surface with BEAST2

mastersimulator

Simulate trees in MASTER and test inferences in BEAST2

msasummary

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

msbd-tutorial

nicola-mueller-talks

ns-tutorial

Model selection using nested sampling tutorial for BEAST 2

ourcodingclub.github.io

The main repository for the Coding Club website

parameterizedbdsky

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

phylocode

pre-columbian-treponema-pallidum-from-brazil

Data and scripts to reproduce the molecular clock dating analyses presented in " Redefining the treponemal history through pre-Columbian genomes from Brazil" (Majandar, Pla-Diaz et al)

regions_of_the_world

List of admin0, admin1 and admin2 regions of the world

rskylinetools

R package implementing function for gridding and plotting skylines.