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icyseq

An extremely simple browser-based multiple sequence alignment viewer.

icytree

Browser-based utility for phylogenetic tree visualisation.

jcred

Simple credentials database manager.

jphylopaint

Java implementation of my non-interactive phylogenetic tree painter.

jsonbrowse

Basic graphical JSON object heirarchy browser

jtrace

A clumsy attempt at ray tracing.

mandelscape

Simple Mandelbrot set exploration program, written to be used as the basis for a COMPSCI 230 Assignment

master

A versatile simulation engine for stochastic population dynamics models.

mcmc.jl

mep-tutorial

Time stamped data tuturial for BEAST 2

mepilabworkshop

One day BEAST 2 workshop delivered to mEpiLab

mess

Display ESS for all parameters in an arbitrary number of BEAST 2 log files.

modelselection

BEAST 2 code for simple model selection.

multitypetree

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

netbeast

Experimental alternative GUI for BEAST 2.

ols

OpenBench LogicSniffer repository

particlefilterresults

BEAST 2 XML and R scripts necessary for reproduction of results in the linked manuscript.

pash

**UGLY** python tool for cwd and directory-local alias management.

pea

PEA Extends Ape - a few function definitions to make it easier to work with time trees in APE

photodist

Estimate distances from stereo photo pairs.

phylotools

Tree/network-wrangling scripts

piratescope

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

pitchfork

Bayesian phylogenetic inference under models supporting explicit polytomies.

populationtraitcoalescent

Compute transmission tree prior probabilities incorporating available host state information.

r0-manuscript-materials

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

raymarching

Ray marching experiment in Scheme

remaster

High-fidelity stochastic tree simulation for BEAST 2.

remaster-master-comparison

Running time comparison for birth-death tree simulations in MASTER and ReMASTER

rolldx

Tiny and simple dice roller.

scotti-tutorial

Transmission tree reconstruction with the structured coalescent