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Phylogenetic Representativeness is a method for estimating adequacy of taxon sampling for phylogenetic studies. Through a series of statistics generated by PhyRe, it is possible to evaluate taxon coverage within a given group.
MAXIMUS is a genome assembly pipeline which takes the best out of multiple reference assemblies and de novo assembly. The benefits of this approach include better assembled repetitive regions, less gaps and higher accuracy for the resultant assembly.
CellPublisher is a free, open source program to improve the navigation of biological pathways. It converts CellDesigner diagrams into fully-featured maps that live inside a browser. The navigation is based on the Google maps API.
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SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.
RefineHMM refines an original hidden Markov model (HMM) to find an optimal fit
against the evolutionary group that the HMM models, and it does this using
through iterative database searches and incremental subsequent adaptation of
the seed set.
A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.
Radar has moved to github (https://github.com/AndreasHeger/radar)
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
A colorized interactive dotplot program designed for pair-wise comparisons of RNA & DNA. The original idea was from the mind of late Prof. William J. Dreyer of Caltech. The idea is to be able to see the "tapestry" of life, which comes alive with color.
FociCounter is a simple and user-friendly program for analysis of gamma-H2AX foci. It allows to determine the number of foci in a single cell, a foci intensity as well as a cell intensity.
Tandem mass spectral peptide identification and validation software, similar to X!Tandem, OMSSA, MyriMatch. Suitable for single hosts through large clusters. Written in Python for simplicity, with performance-critical sections in C++.
Brian is a new simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists.
This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
MIVF - Medical Imaging and Visualization Factory,
is a framework for medical applications. It supplies a platform, in which image processing and 3D visualization algorithms can be employed as reusable components (functional modules or plugins).
"Blue Planet" is a research project simulating the behaviour and darwinian evolution of unicellular lifeforms, each controlled by its own genetic program. Moreover, "Blue Planet Inhabitants" are suited for swarm intelligence and swarm research.
A small simulator for Mendelian genetics, genetic drift, natural selection and random mutations, built on matplotlib and wxpython. A graph will be generated that traces the distribution of genotypes at successive generations.