BioUno's repositories
mrbayes-plugin
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
jenkins-scriptlets
Useful groovy scripts that can be used while using Jenkins-CI for workflow automation
pbs-ansible
An Ansible + Vagrant playbook to set up a PBS Server
beast-plugin
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
biojava-legacy
Legacy BioJava Code
biojava-sandbox
Experimentations with BioJava
biology-data
Data for bioinformatics tools, including input, parameters, and other files
biouno-mvn-repository
A Maven repository for BioUno plug-ins
drmaav2-mock
Reference implementation of the DRMAAv2 C Language Binding
figtree-plugin
FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.
ProvToolbox
Java toolbox to create and convert W3C PROV data model representations
structure-extended-configuration-plugin
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPs, microsatellites, RFLPs and AFLPs. The basic algorithm was described by Pritchard, Stephens & Donnelly (2000). Extensions to the method were published by Falush, Stephens and Pritchard (2003), and (2007) and Hubisz, Falush, Stephens and Pritchard (2009).
structure-harvester-plugin
Structure Harvester plug-in
Structure-Pipeline
Pipeline to run structure on multiple values of K, summarize results with CLUMPP, and create barplot in R
structure-plugin
Structure Plug-in
update-sites-manager
Jenkins plugin to manage UpdateSites, where Jenkins accesses in order to retrieve plugins.
assemblage
Tools for working with second gen assemblies, fasta sequences, etc
biojava
BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
biojs
A library of JavaScript components to represent biological data
GeneticDifferentiation
Code snippets to calculate genetic differentiation in R. See posting at: XXXX
jmol-plugin
Jmol Plug-in