tgvaughan/pitchfork

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GNU General Publi...
Created almost 7 years ago
Updated about 2 years ago

tgvaughan/pitchfork

tgvaughan

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Bayesian phylogenetic inference under models supporting explicit polytomies.

sicm

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

PirateScope

wxPython oscilloscope client for dangerousprototypes.com's Bus Pirate.

icytree

Browser-based utility for phylogenetic tree visualisation.

MultiTypeTree

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

MASTER

A versatile simulation engine for stochastic population dynamics models.

bacter

Bacterial phylogenetics in BEAST 2.

feast

Tasty additions to BEAST 2

BDMM-Prime

Multi-type birth-death-sampling modelling for BEAST 2.

BuildRoster

Employee roster generator.

TimeTrees.jl

Phylogenetic tree type for julia

JsonBrowse

Basic graphical JSON object heirarchy browser

remaster

High-fidelity stochastic tree simulation for BEAST 2.

bioinf702_lectures

Lecture slides for bioinf702

BayesianMCMCLectures

Lectures I gave for a Bayesian statistics minicourse at the University of Hohenheim.

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.

EpiInf

BEAST 2 package for performing inference on epidemiological parameters using the exact likelihood.

Jupyter Notebook

h5shell

Command shell interface for HDF5 scientific data files.

talks

Repository for my web-based talks

HamiltonianTreeDynamics

Rough visualisation of classical mechanics in tree space

PhotoDist

Estimate distances from stereo photo pairs.

mEpiLabWorkshop

One day BEAST 2 workshop delivered to mEpiLab

HK_2018_Slides

Lecture for C3BI workshop in HK, 2018

ModelSelection

BEAST 2 code for simple model selection.

R0-manuscript-materials

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

beast.m4

Some basic m4 macros for BEAST 2 XMLs

HK_2018_MiniProject

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

BSLoader

Easily load R scripts provided by BEAST 2 packages.

icylog

Browser-based BEAST log file analyzer.

TransmissionChainAnalyses

Scripts needed to reproduce phylodynamic analyses from Nadeau et al. 2021.

ceskykrumlov2018_lectures

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