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C Programming Libraries  
An extensive library of C routines for the manipulation of protein structures. The routines are extensively documented within the code, but no separate documentation is currently available. The routines include reading and writing of PDB and CSSR files, rotation, translation, resequencing, calculations, fitting, adding hydrogens, ordering, sequence reading and alignment, etc., etc.
Submitted: Dec 08, 2000
GAlib  
GAlib contains a set of C++ genetic algorithm objects. The library includes tools for using genetic algorithms to do optimization in any C++ program using any representation and genetic operators. The documentation includes an extensive overview of how to implement a genetic algorithm as well as examples illustrating customizations to the GAlib classes.
Submitted: Dec 09, 2000
Macromolecular Geometry  
A library of C source code containing programs for calculating volumes (using the Voronoi method), surfaces contacts, and other parameters relevant to the protein surface. It also contains code for doing a least-squares fit of two structures and for calculating geometrical parameters such as helix axes.
Submitted: Oct 19, 2000
PDBlib  
PDBlib is an extensible object oriented class library, written in C++ for representing the 3-dimensional structure of biological macromolecules. The library models the structural features of proteins,DNA,RNA and complexes thereof, at a level of detail on a par with which can be parsed from a Brookhaven Protein Data Bank (PDB) entry.
Submitted: Dec 09, 2000
OpenChem  
OpenChem is an Open Source program for investigating nanotechnology, molecular structures, machines, and phenomena.
Submitted: Oct 31, 2000
CarthaGene  
CarthaGene is a genetic/radiated hybrid mapping software. CarthaGene looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms based on local search methods (such as simulated annealing, taboo search or genetic algorithms). When data sets are merged, the user can decide whether the sets will share all parameters (order and distances) or only order, allowing for different recombination ratios in each population or a mixture of genetic and radiated hybrid data.
Submitted: Nov 17, 2000
Espoir  
Espoir is a reverse Monte Carlo and pseudo simulated annealing code for ab initio crystal structure determination, either from "scratch" (from a completely random starting model) or by "molecule location" (analogous to the Molecule Replacement method), fitting either to the structure factors amplitudes "Fobs" extracted by powder diffractometry or to single crystal data (not any potential needed). This is a "last chance" program which we recommend to use only after failing with classical methods (Direct and Patterson methods).
Submitted: Sep 11, 2000
e-den  
e-den is a freeware a-life program that supports a unique, digital life-form designed to inhabit cyberspace. The program creates a 2-dimensional world in which organisms equipped with digital bodies and simulated neurons may roam, feed, fight and reproduce. e-den was written in C++, runs on Windows (3.1 or later) and requires a Pentium processor with at least 32 Meg of RAM. e-den is offered as an educational tool or as an experimental playground for those interested in artificial life, biology or neuroscience.
Submitted: Nov 01, 2000
EMBOSS  
EMBOSS is a package of high-quality FREE Open Source software for sequence analysis.
Submitted: Sep 23, 2000
CHIMP  
CHIMP is a generic tool for the modeling of chemical phenomena. Eventually, chemical reaction modeling, molecular mechanics, and quantum mechanic modules will be implemented, along with an easy to use graphical-user interface (GUI). At present, CHIMP has the ability to perform dynamic Monte Carlo simulations on chemical reactions, in particular heterogeneous catalytic reactions.
Submitted: Dec 21, 2000
Phylo_win  
Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.
Submitted: Oct 15, 2000
Macromolecular Geometry  
A library of source code for doing a variety of calculations on protein structures and sequences.
Submitted: Sep 06, 2000
K2D  
An algorithm for the estimation of the percentages of protein secondary structure from UV circular dichroism spectra using a Kohonen neural network with a 2-dimensional output layer. You can either use k2d via a web server or get the program and run it on your machine.
Submitted: Jan 06, 2001
NAMD  
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.
Submitted: Sep 05, 2000
The Object Technology Framework  
The Object Technology Framework (OTF) is a system for easily generating powerful C++ classes tailored to the needs and specifications of biochemical application developers.
Submitted: Dec 09, 2000
HARDY  
HARDY contains program and documentation by Dr. Sunwei Guo, for Monte Carlo estimation of P-values in a sparse two-dimensional contingency table, or for Hardy Weinberg equilibrium.
Submitted: Oct 20, 2000
Estimation of Evolutionary Distance  
A method for estimating the most general reversible substitution matrix corresponding to a given collection of aligned DNA sequences. This matrix can then be used to calculate evolutionary distances between pairs of sequences in the collection.
Submitted: Oct 08, 2000
Treetool  
Treetool is an interactive tool for displaying, editing, and printing phylogenetic trees. The tree is displayed visually on screen, in various formats, and the user is able to modify the format, structure, and characteristics of the tree. Trees may be viewed, compared, formatted for printing, constructed from smaller trees, etc...
Submitted: Oct 15, 2000
POPGENE  
POPGENE is a joint project development by Francis Yeh , Rongcai Yang and Timothy Boyle. It is a user-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers. This package provides the Windows graphical user interface that makes population genetics analysis more accessible for the casual computer user and more convenient for the experienced computer user. Simple menus and dialog box selections enable you to perform complex analyses and produce scientifically sound statistics, thereby assisting you to adequately analyze population genetic structure using the target markers.
Submitted: Oct 15, 2000
NJplot  
NJplot is able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the Phylip package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Submitted: Oct 15, 2000
Meta-MEME  
Meta-MEME is a software toolkit for building and using motif-based hidden Markov models of DNA and proteins. The input to Meta-MEME is a set of similar protein sequences, as well as a set of motif models discovered by MEME. Meta-MEME combines these models into a single, motif- based hidden Markov model and uses this model to produce a multiple alignment of the original set of sequences and to search a sequence database for homologs.
Submitted: Nov 05, 2000
Weighbor  
Weighbor is a weighted version of Neighbor Joining that gives significantly less weight to the longer distances in the distance matrix. The weights are based on variances and covariances expected in a simple Jukes-Cantor model. The criterion for which pair is joined is based on a likelihood function on the distances. The resulting trees are less perturbed by adding distant taxa compared to Neighbor Joining, and negative branch lengths are avoided. The method does not suffer from long branch attraction as maximum parsimony and other methods do. The method is much faster than maximum likelihood, usually faster than maximum parsimony, and a lot slower than Neighbor Joining.
Submitted: Oct 08, 2000
Altruist  
Altruist is a software package for simulation of genetic evolution in structured or viscous populations. The program is free to use (public license). Several simulation models are supported for the simulation of group selection, peak shifts, Wright's shifting balance, punctuated equilibria, speciation, and metaadaptation.
Submitted: Nov 01, 2000
DIALIGN  
DIALIGN is a novel method for multiple alignment developed by Burkhard Morgenstern et al. While standard alignment programs 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. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families.
Submitted: Oct 20, 2000
SHAPE  
The SHAPE package consists of two programs: surfractal which calculates fractal atomic density, and maxaccess which calculates maximal sphere accessibility. Together they can be used to analyze structure and chemistry at the molecular surface. These programs can also be used easily as front ends for graphics programs such as Insight II and AVS. Along with the SHAPE package, SDSC will be distributing the SHAPE filter programs for Insight and AVS. This software will be free for academic users, but you must sign and return a license before accessing SHAPE.
Submitted: Oct 08, 2000
Ghemical  
Ghemical is a computational chemistry software package released under the GNU GPL. It has a graphical user interface (in fact, a couple of them), and it can do all-atoms molecular mechanics (there is an experimental Tripos 5.2-like force field for organic molecules), and reduced protein models using a recently developed method (submitted for publication). Geometry optimization, molecular dynamics and some visualization tools are currently available. If quantum-mechanical calculations are needed, Ghemical can be directly linked into the quantum chemistry program MPQC (which is also distributed under GNU GPL). Therefore Ghemical can serve as a graphical front-end for the MPQC program, currently providing various 3D-plots for electron densities, molecular orbitals and molecular orbital densities.
Submitted: Oct 18, 2000
Software for Analyzing Phylogenetic Trees  
Software is available to build phylogenetic trees from data sets. For each collection of four taxa, the best tree for those species alone is computed either by the criterion of Maximum Parsimony or by the criterion of Higher Order Parsimony, which introduces a correction to Maximum Parsimony that reduces the effect of long-branch attraction.
Submitted: Oct 15, 2000
Electronic Periodic Table of the Elements  
The Electronic Periodic Table of the Elements, originaly written in C and still in C, can be downloaded and used. It includes sound files (which you may choose not to install) that give element names and definitions out loud.
Submitted: Dec 22, 2000
OPIUM  
This page is concerned with solution equilibria analysis, determination of chemical model, determination of equilibrium (stability, formation, protonation, dissociation, association) constants using potentiometry, UV/VIS spectrophotometry, NMR spectroscopy, polarography, vapour-pressure osmometry, capillary zone electrophoresis, and other useful methods with the OPIUM computer program.
Submitted: Dec 22, 2000
CORINA  
A rule and data based system, that automatically generates three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table or linear code, and which is powerful and reliable to convert large databases of several hundreds of thousand or even millions of compounds.
Submitted: Dec 16, 2000
EGO  
EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers. Supported parallel machines include the Hitachi SR8000, CRAY-T3E, IBM-SP2, Fujitsu VPP700, Parsytec-CC under PARIX and inhomogeneous clusters of UNIX workstations under PVM or MPI. EGO also runs sequentially on any decent UNIX workstation; even Windows95/NT PC's (with a GNU-C compiler) can be used.
Submitted: Oct 18, 2000
ChemCalc  
ChemCalc is a calculator that is more oriented towards chemistry. Although starting out as a console app, it is a hope that an X11 interface will be designed at a later time.
Submitted: Dec 21, 2000
MolScript  
MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
Submitted: Sep 30, 2000
NMRPipe  
NMRPipe provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. It is currently used in over 300 academic and commercial laboratories.
Submitted: Oct 09, 2000
RRTree  
RRTree is a program for relative-rate tests. It compares substitution rates between DNA or protein sequences grouped in phylogenetically defined lineages: Relative-Rate Tests with a tree.
Submitted: Sep 19, 2000
ChemApp  
ChemApp© provides the powerful calculation capabilities of ChemSage in the form of a programmer's library. It consists of a rich set of subroutines which provides all the necessary tools for the calculation of complex multicomponent, multiphase chemical equilibria and the determination of the associated energy balances.
Submitted: Jan 06, 2001
MolScript  
MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
Submitted: Oct 08, 2000
MSMS  
MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces.
Submitted: Sep 12, 2000
OpenRasMol  
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. This site is provided for the convenience of users and software developers of open source versions of RasMol.
Submitted: Dec 17, 2000
XMolCalc  
This is intended to be the chemists version of the X desktop calculator. It's customizable and the C-code is highly transparent.
Submitted: Dec 22, 2000
VASP Data Viewer  
This is a scientific visualization package for examining output files generated by the Vienna Ab-initio Simulation Package, a package for performing ab-initio quantum-mechanical molecular dynamics using pseudopotentials and a plane wave basis set. It displays iso-surfaces and slices of a three-dimensional data set, along with the atoms that make up the molecule the calculations were performed for, and allows symbolic bonds to be inserted between them.
Submitted: Dec 22, 2000
VEGA  
VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D structures of molecules.
Submitted: Oct 17, 2000
ASC  
EMBL's Analytic Surface Calculation Service, calculates the surface of a given PDB structure.
Submitted: Oct 19, 2000
InSegT  
In subdirectory InSegT are C++ programs (and a readme file, readme_insegt) for constructing feasible haplotype configurations and the corresponding segregation types on pedigrees. The haplotype configuration minimizes recombinations on the pedigree.
Submitted: Oct 20, 2000
TOPAL  
The TOPAL package checks for evidence of past recombination events, by looking for changes in the inferred phylogenetic tree TOPology between adjacent regions of a multiple sequence ALignment
Submitted: Oct 15, 2000
Vienna RNA Package  
A package for RNA secondary structure prediction and comparison consisting of a code library and several stand-alone programs for prediction and comparison.
Submitted: Sep 06, 2000
WORLDMAP  
WORLDMAP is easy-to-use software for exploring geographical patterns in diversity, rarity and conservation priorities from large biological datasets.
Submitted: Nov 01, 2000
BAMBE  
Bayesian Analysis in Molecular Biology and Evolution (BAMBE) is a free software package for the Bayesian analysis of phylogenies. The package includes programs for analyzing aligned DNA or RNA sequence data and allows data sets with gaps or indeterminate sites.
Submitted: Oct 15, 2000
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. Separate module DIFFC, included into the DASHA software, performs hydrodynamic calculations for proteins with known spatial structure. All input and output data could be easily presented in PostScript format.
Submitted: Oct 15, 2000
NAMD  
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code.
Submitted: Dec 08, 2000
Progeny  
Progeny Software allows you to view and analyze family history in both pedigree and data formats.
Submitted: Nov 17, 2000
Caspar  
CASPAR is an exploratory program to study the genetics of complex (polygenic) diseases. Given genetic information about families at multiple loci, it allows the user to explore hypotheses about how different factors may be involved in disease susceptibility of polygenic diseases. It semi-automatically and rapidly does an extended form of Affected Sibling Pair (ASP) tests for subset of families defined by their characteristics at one or more loci. The main advantage of CASPAR over othe ASP software packages is that CASPAR allows the user to do linkage analysis at one locus, conditional on the status of another locus, while properly accounting for the multiple statistical testing that is being done.
Submitted: Nov 17, 2000
DIALIGN  
DIALIGN is a novel 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. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families.
Submitted: Dec 03, 2000
FSAP  
The Fristensky Sequence Analysis Package (formerly Cornell Sequence Analysis Package) has proven to be a versatile, reliable, and highly portable suite of programs for sequence analysis. At the heart of the package is NUMSEQ a sequence manipulation program that provides a large number of options for presentation of sequence data, as well as facilitating simulation of operations such as translation, subcloning and ligation.
Submitted: Oct 08, 2000
PovChem  
PovChem takes three-dimensional chemical information in the Protein Data Bank format, constructs a model, and outputs a plain-text file that contains that model in the POV-Ray format.
Submitted: Sep 12, 2000
Sparky  
Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.
Submitted: Oct 09, 2000
BOREL  
BOREL is a set of programs for evaluating sibship relationships, written by Dr. Ian Painter (1995).
Submitted: Oct 20, 2000
fastDNAml  
fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program. fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable.
Submitted: Oct 15, 2000
HAPPY  
A software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals.
Submitted: Nov 17, 2000
NAB  
Nucleic acid builder (nab) is a high-level language that facilitates manipulations of macromolecules and their fragments. nab uses a C-like syntax for variables, expressions and control structures (if, for, while) and has extensions for operating on molecules (new types and a large number of builtins for providing the necessary operations).
Submitted: Sep 30, 2000
PAML  
PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
Submitted: Sep 05, 2000
RHMAPPER  
RHMAPPER is a software package for creating radiation hybrid maps. It was designed to accommodate very large scale radiation hybrid maps, and has been used successfully to create whole genome maps containing thousands of markers at the Whitehead Institute/MIT Center for Genome Research.
Submitted: Sep 19, 2000
ANCML  
The program ANCML estimates ancestor states for a continuous trait, and provides a "standard error" for the marginal distribution of each estimate.
Submitted: Sep 05, 2000



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