Adun is an extensible biomolecular simulation program that includes data management and analysis capabilities.
Clarrhmos is a cell automata description language and simulation program for models of myocardial electrophysiology.
This package offers a GUI interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence- and profile-alignments to analyse the results. The sequence alignment is displayed in a window on the screen.
Consed is a graphical Tool for Editing Phrap Assemblies.
Constance System for Online EEG (ConSole) is a free and open-source application to build and run realtime EEG experiments.
CONUS is software for the exploration of lightweight stochastic context free grammars.
CTSim simulates the process of transmitting X-rays through phantom objects. These X-ray data are called projections. CTSim reconstructs the original phantom image from the projections using a variety of algorithms. Additionally, CTSim has a wide array of image analysis and image processing functions.
DIALIGN is a software program for multiple alignment developed by Burkhard Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used.
Finomaton lets you comfortably draw and typeset finite state machines (automata). It outputs plain MetaPost-code which can be transformed to PostScript and subsequently included in your TeX and LaTeX documents for excellent typesetting quality.
FIRM is an interactive program (fortran) for calculating NOEs of a structural model using the relaxation matrix approach.
FreeDiams is a program for making prescriptions of pharmaceutical drugs and testing their interactions. It is the result of building the FreeMedForms prescriber plugins into a standalone application.
GTdb is a modular genotype database for all markers and organisms. The database has core which captures information common to different variation measurements and extensions to method and instrument specific data.
gtkdive was written to learn about the Buehlmann ZH-L16 model that deals with accumulation of inert gas in body tissues.
MetaPath is a tool for the analysis of metabolic pathway and associated visualisation of experimental data. Built on the MetaCyc database it provides an interactive map in which multiple pathways can be simultaneously visualised.
Micro-Manager is a software package for microscope image acquisition. It controls a number of scientific grade cameras, shutters, filter wheels, stages, and other devices. It enables the acquisition of time-lapses, z-stacks, and multi-channel images.
mkESA is a program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on an implementation of Manzini's lightweight Deep-Shallow algorithm, which can also utilize multiple CPUs/cores for extra performance.
MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. Read more
OpenVista is the open-source version of VistA, which is a healthcare information system developed by the U.S. Department of Veterans Affairs (the "VA") to drive all their hospitals and clinics.
(commercial) Paup is for the inference of evolutionary trees.
Pyvox (formerly known as BBLimage) is a set of software tools for medical image processing, particularly skull stripping and segmentation of MR brain images; tools to support other applications may be added later. These tools are intended to support researchers who need to prototype new image analysis algorithms or to develop automated image analysis tools for specific image analysis applications.
QDist implements a sub-cubic algorithm for computing the quartet distance between between general trees (i.e. the trees are not required to be binary).
ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. It supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, and XML).
SIBsim4 is an extensive rewrite of the sim4 program to improve execution speed and provide more informative output. Written in C, mainly targeted at Linux and Unix.
SimThyr is a continuous simulation program for pituitary-thyroid feedback control.
simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. Read more
SPINA is software for determining constant structure-parameters of endocrine feedback control systems from hormone levels obtained in vivo.
SU-ALIGN is a software package for identifying, aligning, masking and visualizing archaeal 16S, bacterial 16S and eukaryotic 18S small subunit ribosomal RNA (SSU rRNA) sequences. It includes and uses the Infernal software package for generating alignments based on the conserved secondary structure and sequence of SSU rRNA.
SwissParser allows you to build parsers for typical bioinformatics flat-file "database"
ThermonucleotideBLAST is a software program for searching a target database of nucleic acid sequences using an assay specific query that is based on biochemical assays (i.e. a pair of oligonucleotide sequences representing PCR primers or Padlock probes, a triplet of oligos representing PCR primers and a TaqMan probe, or a single oligo representing a hybridization probe). Unlike existing programs (i.e. BLAST) which use heuristic measures of sequence similarity for identifying matches between a query and target sequence, ThermonucleotideBLAST uses free energy and melting temperature.
TREE-PUZZLE (previously known as PUZZLE) is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Read more
TreeView X is an open source and multi-platform program to display phylogenetic trees. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). Read more
Trio is a conversion program that provides the ability to read and write molecular dynamics trajectory files in several common formats. It is a small standalone program, and should be easy to compile and run on almost any system.