| SimWalk2
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SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), and identity by descent (IBD) analyses on any size of pedigree. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms to perform these multipoint analyses.
Submitted Nov 17, 2000
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| DelPhi
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DelPhi is a program which uses finite difference method to solve the Poisson-Boltzmann equation for molecules of arbitrary shape and charge distribution.
Submitted Oct 18, 2000
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Total Visits: 32
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| DynaFit
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The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance).
Submitted Oct 08, 2000
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| DYNAMO
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DYNAMO is a library of Fortran 90 modules that has been designed for the simulation of molecular systems using molecular mechanical (MM) and hybrid quantum mechanical (QM)/MM potential energy functions.
Submitted Oct 18, 2000
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Total Visits: 23
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| Genometric Analysis Simulation Program (G.A.S.P.)
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The Genometric Analysis Simulation Program (G.A.S.P.) is a software tool that can generate samples of family data based on user specified genetic models. Data generated can be as simple as a single sample of random individuals with a single normally distributed trait or as complex as thousands of samples of extended families with multiple traits based on a linear combination of major locus, polygenic, common sibship environment and covariate components. Traits can be generated based on a number of user specified components, and components can be unique to a single trait or shared by multiple traits.
Submitted Oct 20, 2000
Updated Jan 06, 2001
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Total Visits: 22
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| Dirac
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DIRAC is a FORTRAN (and a bit of C) code for relativistic molecular calculations based on the Dirac-Coulomb Hamiltonian. It solves the the 4-component Dirac-Hartree-Fock (DHF) equations by the Self Consistent Field (SCF) iterative procedure and provides tools for analysis of the converged wave function.
Submitted Oct 18, 2000
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Total Visits: 17
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| Raster3D
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Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.
Submitted Oct 08, 2000
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| ORTEP-III
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The Oak Ridge Thermal Ellipsoid Plot (ORTEP) program is a computer program for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations which aid in the visualization of complex arrangements of atoms and their correlated thermal motion patterns.
Submitted Sep 12, 2000
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| AMSOL
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This software calculates the free energies of solvation in aqueous solutions, charge models for partial atomic charges of gas-phase molecules and of solutes in alkane solvents and models for free energies of solvation and partial atomic charges in water or in any organic solvent.
Submitted Sep 05, 2000
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| CINEMA
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CINEMA is a Colour INteractive Editor for Multiple Alignments. The program allows visualisation and manipulation of both protein and DNA sequences.
Submitted Sep 04, 2000
Updated Sep 20, 2000
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| Statistical Genetics Software
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MENDEL is a program for the genetic analysis of human pedigree data under models involving a small number of loci. FISHER is a program for the genetic analysis of classical biometric traits like blood pressure or height that are caused by a combination of polygenic inheritance and complex environmental forces. SEARCH is a subprogram for function minimization. SPERM is a program for the analysis of sperm typing data.
Submitted Sep 19, 2000
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Total Visits: 7
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| Haplo
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Haplotyping with computation of conditional probabilities.
Submitted Nov 17, 2000
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Total Visits: 5
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| TINKER
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The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for polypeptides.
Submitted Sep 15, 2000
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Total Visits: 5
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| PHASES
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PHASES is a package of computer programs designed to compute phase angles for diffraction data from macromolecular crystals.
Submitted Sep 12, 2000
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Total Visits: 4
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| GAMESS
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The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. GAMESS is maintained by the members of the Gordon research group at Iowa State University.
Submitted Sep 05, 2000
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Total Visits: 3
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| SHELX
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SHELX is a set of programs for crystal structure determination from single-crystal diffraction data.
Submitted Dec 10, 2000
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Total Visits: 3
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| Test_shotgun
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Test_shotgun is a Fortran program which simulates a shotgun sequencing project. It is a handy tool for estimating not only how much work must be done (or remains to be done) for a given project, but also how much it will cost. It simulates projects up to 1 Mbp directly in memory. For projects larger than that it simulates it in 1 Mbp region and then scales the results. It is known to compile and run on OpenVMS, Digital Unix, and IRIX.
Submitted Sep 30, 2000
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| PREPI
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PREPI is a molecular graphics program which can be used to EASILY produce and interactively manipulate many different types of molecular representations (cartoons) as well as providing quantative information on secondary structural topology. The program is not just limited to proteins, but can also show cartoon representations of NUCLEIC ACIDS.
Submitted Sep 12, 2000
Updated Dec 17, 2000
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| ASAD
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ASAD is a software package developed for creating and integrating chemistry schemes in atmospheric models without the need to write any FORTRAN code to solve the chemical rate equations.
Submitted Dec 21, 2000
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| bioWidgets
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The bioWidgets toolkit is a collection of Java Beans(tm) used for development of graphics applications and/or applets in the genomics domain.
Submitted Oct 17, 2000
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Total Visits: 1
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