Tim Vaughan (@tgvaughan)
github

tgvaughan

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Top repositories

1

sicm

Unofficial HTML version of Sussman and Wisdom's "Structure and Interpretation of Classical Mechanics"
HTML
81
star
2

PirateScope

wxPython oscilloscope client for dangerousprototypes.com's Bus Pirate.
Python
43
star
3

icytree

Browser-based utility for phylogenetic tree visualisation.
JavaScript
37
star
4

MultiTypeTree

BEAST 2 package which provides support for multi-type trees: phylogenetic trees on structured populations.
Java
22
star
5

MASTER

A versatile simulation engine for stochastic population dynamics models.
Java
22
star
6

bacter

Bacterial phylogenetics in BEAST 2.
Java
17
star
7

feast

Tasty additions to BEAST 2
Java
11
star
8

BDMM-Prime

Multi-type birth-death-sampling modelling for BEAST 2.
Java
6
star
9

BuildRoster

Employee roster generator.
Python
5
star
10

TimeTrees.jl

Phylogenetic tree type for julia
Julia
5
star
11

JsonBrowse

Basic graphical JSON object heirarchy browser
Java
5
star
12

remaster

High-fidelity stochastic tree simulation for BEAST 2.
Java
4
star
13

bioinf702_lectures

Lecture slides for bioinf702
HTML
3
star
14

BayesianMCMCLectures

Lectures I gave for a Bayesian statistics minicourse at the University of Hohenheim.
JavaScript
3
star
15

dvtm

Fork of dvtm (http://www.brain-dump.org/projects/dvtm) that provides simple runtime configuration of key bindings and other basic options via an ini-like config file.
C
3
star
16

EpiInf

BEAST 2 package for performing inference on epidemiological parameters using the exact likelihood.
Jupyter Notebook
3
star
17

h5shell

Command shell interface for HDF5 scientific data files.
Python
2
star
18

talks

Repository for my web-based talks
HTML
2
star
19

HamiltonianTreeDynamics

Rough visualisation of classical mechanics in tree space
Processing
2
star
20

PhotoDist

Estimate distances from stereo photo pairs.
Java
1
star
21

mEpiLabWorkshop

One day BEAST 2 workshop delivered to mEpiLab
JavaScript
1
star
22

pitchfork

Bayesian phylogenetic inference under models supporting explicit polytomies.
Java
1
star
23

HK_2018_Slides

Lecture for C3BI workshop in HK, 2018
JavaScript
1
star
24

ModelSelection

BEAST 2 code for simple model selection.
Java
1
star
25

R0-manuscript-materials

Supplemental files and data for the manuscript "Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data".
R
1
star
26

beast.m4

Some basic m4 macros for BEAST 2 XMLs
M4
1
star
27

HK_2018_MiniProject

Instructions and data for student mini-project at the 2018 C3BI course on molecular phylogenetics.
Python
1
star
28

BSLoader

Easily load R scripts provided by BEAST 2 packages.
R
1
star
29

icylog

Browser-based BEAST log file analyzer.
JavaScript
1
star
30

TransmissionChainAnalyses

Scripts needed to reproduce phylodynamic analyses from Nadeau et al. 2021.
R
1
star
31

ceskykrumlov2018_lectures

Talks presented at the 2018 Workshop on Population and Speciation Genomics, Cesky Krumlov
JavaScript
1
star