Software

This page contains a list of software projects that I am currently involved with as part of my research. If you are interested in any of my older software projects, ask google, but if it isn't listed on this page I will not promise any support on it.

Phylogenetic Trees

Construction and Comparison

• RapidNJ — Fast and memory efficient neighbour-joining tree construction.
• QuickJoin — Fast neighbour-joining tree construction.
• QDist — Computation of the quartet distance between evolutationary trees.
• Split-Dist — Computation of the split distance between evolutationary trees.
• CoAnnealing — A tool for inferring local phylogenies. Developed in colaboration with Bioinformatics ApS.

Manipulation and Visualisation

• Newick — A python parser for the Newick tree format.
• DrawTree — A program for translating Newick format into graphical formats.

Population genomics

• CoalHMM — Tool for infering speciation time and ancestral population sizes

Simulators

• CoaSim — A tool for simulating the coalescent process. Developed in colaboration with Bioinformatics ApS.

Association Mapping

• SNPfile — A library and API for manipulating large SNP datasets with associated meta-data in an I/O efficient binary file format.
• SMA — A small collection of tools that calculates the single marker association between individual SNP markers and a case/control dichotomy.
• GeneRecon — An MCMC based statistical tool for association mapping. Developed in colaboration with Bioinformatics ApS.
• HapCluster++ — An MCMC based statistical tool for association mapping.
• CoAnnealing — A tool for inferring local phylogenies. Developed in colaboration with Bioinformatics ApS.
• Blossoc — A whole-genome association mapping tool.

Hidden Markov models

• HMMlib — library for hardware accelerated HMM analysis.

Programming

• dProg — a programming language for specifying dynamic programming algorithms.

Python

• Newick — A parser for the Newick tree format.
• fasta.py — Parser routines for reading fasta files.
• gde.py — Parser routines for reading GDE files.
• SuffixTree — Python bindings for a suffix tree.
• ClustalW Wrapper — Python wrapper for the Clustal W tool.