Open Source Linux Bio-Informatics Software

The aim of the BioWeka project is to add bioinformatics functionalities such as e.g. alignments to the popular machine learning framework Weka.

Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.

Several RNA and protein structure volume calculation tools.

APoDIx is a Portable Bio-Database Index system. It retrieves biological database information from the website of Oxford Journals, save them in a local position, and provides a viewer for display and search the information.

A C++ library for Bayesian computation, including a collection of more generally-applicable utilities.

This software provides accession to multiple biological applications and databases at different servers.

BioGeoTools is a Java based package that is aimed at providing a program and libraries for biogeorgaphy analyses.

Common Interface for NMR structure Generation.

A collection of Perl modules and programs for bioinformatics. Design intention is to make most common, straight-forward tasks in computational biology as simple, and portable, as possible.

The DNA Sequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or assembly).

GODASM is the brief of ".Gff Organized Data Analysis System for Microarray Studies". Private programs, GODA system, had been successful developed in 2008 at CGMH,Taiwan. Now the project will transfer GODAs to open-source based system.

The goal of the GeneText project is the development of a software package that will enable users to dynamically generate an information summary page from multiple sources given a search term. Fields of interest are biology, genetics and bioinformatics.

A program to model HapMap haplotypes in genetic association studies using tag SNP genotypes. Please visit http://www.ucd.ie/genepi/hapmixmap for more details.

Set of iterative filters.

Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.

>>> MIA has been moved to GitHub! <<< Please use the new Location: https://github.com/udo-stenzel/mapping-iterative-assembler =========================================================

Bioinformatics is commonly understood as work with the DNA and protein sequences. However databases and computational analysis were tried on other objects far before these sequences became widely available. This work is about analysis of spatial movement

The Neural Assembly Simulation Environment (NASE) is a collection of routines written in the Interactive Data Language (IDL) by Research Systems Inc. It provides routines to simulate neural networks and to visualize those networks' behavior.

Featurama, superceding ProbePicker, is a bioinformatics program used to generate short probes from large datasets for use in DNA microarray experiments. A new project, BioSap, will extend the functionality of featurama.

UPDATE: After some bug fixes, I've ditched Pysimony for Javamony: https://sourceforge.net/projects/javamony/ Given Python's beauty, I know that someday I will have to finish Pysimony. A student's first attempt at a phylogenetic inference program, written in the simplistic yet elegant Python. Pysimony reads a FASTA file (only ATGC accepted) specified as its only argument. Basic testing has shown that it is slow, inaccurate and most definitely inefficient. An unlikely-to-be-the-most-parsimonious tree is printed upon completion in basic Newick tree format. As all parts of the program are the original work of a beginner programmer, this may represent one of the worst approaches to solving the phylogenetic problem. I have clearly avoided object-oriented programming. Nevertheless, I distribute this imagining it might someday be slightly educational or at least provide a laugh at the pathetic attempt it makes to reinvent the wheel

SpOK - The Spectrum Organisation Kit, a program for the organisation and visualisation of spectral data written in Java. Sorry - this project is not being continued. All functionality was integrated into the Bioclipse project...

This project has moved to http://code.google.com/p/synthetic/

Zherlock has now changed name to SciCraft and no longer hosted on sourceforge. Visit our new site at http://www.scicraft.org

bc_scatterplot is a scatterplot plugin for the bioclipse project

defunct