Pinned Repositories
bacter
Bacterial phylogenetics in BEAST 2.
BDMM-Prime
Multi-type birth-death-sampling modelling for BEAST 2.
feast
Tasty additions to BEAST 2
icytree
Browser-based utility for phylogenetic tree visualisation.
JsonBrowse
Basic graphical JSON object heirarchy browser
MASTER
A versatile simulation engine for stochastic population dynamics models.
MultiTypeTree
BEAST 2 package which provides support for multi-type trees: phylogenetic trees on structured populations.
PirateScope
wxPython oscilloscope client for dangerousprototypes.com's Bus Pirate.
remaster
High-fidelity stochastic tree simulation for BEAST 2.
sicm
Unofficial HTML version of Sussman and Wisdom's "Structure and Interpretation of Classical Mechanics"
tgvaughan's Repositories
tgvaughan/sicm
Unofficial HTML version of Sussman and Wisdom's "Structure and Interpretation of Classical Mechanics"
tgvaughan/icytree
Browser-based utility for phylogenetic tree visualisation.
tgvaughan/MASTER
A versatile simulation engine for stochastic population dynamics models.
tgvaughan/MultiTypeTree
BEAST 2 package which provides support for multi-type trees: phylogenetic trees on structured populations.
tgvaughan/bacter
Bacterial phylogenetics in BEAST 2.
tgvaughan/feast
Tasty additions to BEAST 2
tgvaughan/BDMM-Prime
Multi-type birth-death-sampling modelling for BEAST 2.
tgvaughan/remaster
High-fidelity stochastic tree simulation for BEAST 2.
tgvaughan/EpiInf
BEAST 2 package for performing inference on epidemiological parameters using the exact likelihood.
tgvaughan/pitchfork
Bayesian phylogenetic inference under models supporting explicit polytomies.
tgvaughan/talks
Repository for my web-based talks
tgvaughan/TransmissionChainAnalyses
Scripts needed to reproduce phylodynamic analyses from Nadeau et al. 2021.
tgvaughan/icylog
Browser-based BEAST log file analyzer.
tgvaughan/mess
Display ESS for all parameters in an arbitrary number of BEAST 2 log files.
tgvaughan/R0-manuscript-materials
Supplemental files and data for the manuscript "Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data".
tgvaughan/ali
Command-line interface to some basic Biopython alignment manipulation functions.
tgvaughan/bang
Bang! Adding Turing Completeness to your config files since 2020.
tgvaughan/bdmm
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
tgvaughan/beast2
Bayesian Evolutionary Analysis by Sampling Trees
tgvaughan/BeastFX
GUIs for BEAST using Java FX to make things more pretty.
tgvaughan/BiozentrumTalk
tgvaughan/carlo-tim-sampling-study
tgvaughan/CBAN
releases of beast2 packaged zip files in a reliable location
tgvaughan/Chip
Graphical construction and modification of BEAST 2 XML files.
tgvaughan/figtree
Automatically exported from code.google.com/p/figtree
tgvaughan/HIV_multiple_clusters_NSW
HIV phylodynamics of multiple clusters from NSW
tgvaughan/icyseq
An extremely simple browser-based multiple sequence alignment viewer.
tgvaughan/ParticleFilterResults
BEAST 2 XML and R scripts necessary for reproduction of results in the linked manuscript.
tgvaughan/PhyloTools
Tree/network-wrangling scripts
tgvaughan/remaster-master-comparison
Running time comparison for birth-death tree simulations in MASTER and ReMASTER