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Adun Adun is an extensible biomolecular simulation program that includes data management and analysis capabilities. Blixem BLast matches In an X-windows Embedded Multiple alignment: n interactive browser of pairwise Blast matches that have been stacked up in a "master-slave" multiple alignment. Clarrhmos Clarrhmos is a cell automata description language and simulation program for models of myocardial electrophysiology. Clustal X 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 Consed is a graphical Tool for Editing Phrap Assemblies. CTSim 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. DASHA DASHA is an interactive program designed to investigate dynamics of biomolecules, for which data of 15N or 13C heteronuclear relaxation are available from NMR measurements. DelPhi DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast (the best relaxation parameter is estimated at run time), accurate (calculation of the electrostatic free energy is less dependent on the resolution of the lattice) and can handle extremely high lattice dimensions. DIALIGN 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 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 FIRM is an interactive program (fortran) for calculating NOEs of a structural model using the relaxation matrix approach. GTdb 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 gtkdive was written to learn about the Buehlmann ZH-L16 model that deals with accumulation of inert gas in body tissues. Micro-Manager 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. NDEE NDEE is for the evaluation of n-dimensional NMR-data. The ability to combine structural and dynamic information is one of the most important attributes of NMR in structural molecular biologic context. O O is a general purpose macromolecular modelling environment. The program is aimed at scientists with a need to model, build and display macromolecules. Unlike other molecular modelling programs, such as FRODO, O is a graphical display program built on top of a versatile database system. All molecular data is kept in this database, in a predefined datastructure. OpenVista 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. Paup (commercial) Paup is for the inference of evolutionary trees. Pyvox 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 QDist implements the O(n log˛ n) time method for computing the quartet distance between unrooted evolutionary trees. SIBsim4 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. ThermonucleotideBLAST 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. Trio 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.
