biouno/update-sites-manager
Jenkins plugin to manage UpdateSites, where Jenkins accesses in order to retrieve plugins.
Developer Profile
biouno
Discovered public repositories for biouno in the GitHub catalog.
biouno/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.
biouno/structure-harvester-plugin
Structure Harvester plug-in
biouno/clumpp-plugin
Public repository.
biouno/biouno.github.io
BioUno web site
biouno/pbs-plugin
Jenkins PBS plug-in
biouno/pbs-java-api
PBS Java API
biouno/structure-plugin
Structure Plug-in
biouno/image-gallery-plugin
Jenkins Plug-in for displaying galleries of images from a job workspace
biouno/biouno-mvn-repository
A Maven repository for BioUno plug-ins
biouno/r-plugin
r-plugin
biouno/r-sandbox
R Sandbox
biouno/mega-pairwise-distance-matrix2column
MEGA pairwise distance matrix2column
biouno/pbs4java
Fork of pbs4java
biouno/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).
biouno/biology-data
Data for bioinformatics tools, including input, parameters, and other files
biouno/biojava-legacy
Legacy BioJava Code
biouno/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.
biouno/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.
biouno/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.