Biotechnology Software

This page contains links to biotechnology-related non-commercial software available via the Internet. These links are provided as a service to NBIF visitors. The software packages are the products of their respective authors, and NBIF makes no representations as to their fitness for use in a given application.

The software is grouped into the following categories:

Biomedical Biophysics Chemistry Molecular Biology Genetic Analysis PCR Phylogenetic Analysis Protein Structure Prediction Sequence Analysis Molecular Modeling Numerical Analysis

Software Reviews Software Repositories and Search Engines Biotechnology Related General Repositories Support Tools and Utilities Graphics Graphing and Statistical Analysis Miscellaneous Typefonts Web Authoring X Windows

Categories

Biomedical

• Genesis - This program runs simulation programs of different neural systems.
• Gideon (C.Y Informatics) - Diagnosis and reference in various medical situations is the purpose of this interactive computer program.
• OSIRIS (UIN) - This software package is for general medical image manipulation and analysis.
• XCOSM (Washington Univ. Biomedical Computer Laboratory) - This program implements two algorithms in computational optical sectioning microscopy, improving overall lighting quality.

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Biophysics

• CCP4 (Daresbury Laboratory) - The CCP4 Program Suite is an integrated set of programs for protein crystallography. It is distributed in source form (mostly Fortran), supported for VMS and various Unix platforms.
• Naccess (S. Hubbard and J. Thornton, UMIST) - A stand alone program that calculates the accessible area of a molecule from a PDB format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids.
• NAExplor: Nucleic Acid Exploration (M. Assmann, Friedrich Schiller Univ. Jena) - A tool for converting and analyzing coordinates and NMR-derived distance restraints files for use with the software packages MARDIGRAS, AMBER, CHARMM, and XPLOR.
• Torsion (ACRM) - Torsion is a program for calculating phi, psi, omega and C-alpha pseudo-torsions.

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Chemistry

• Alkane (Bio-Rad Laboratories) - This program constructs alkanes by IUPAC rules.
• AMSOL (Oxford Molecular Group) - 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.
• BALLROOM - A program that is a visualization tool for a set of particles. Particles are displayed as balls projected on two dimensions, and can display thousands of particles.
• BOD Magic (Pharmaceuticalonline) - Automated hardware and software system capable of measuring dissolved oxygen, calculating BOD and reporting results.  
• CCP4 (UK Biotechnology and Biological Sciences Research Council) - An integrated set of programs for protein crystallography which performs Patterson search and refinement, isomorphous and molecular replacement, and structure refinement.
• ChemDraw plugin (CambridgeSoft) - A program that can function as a remote database query client. A structure can be drawn and sent over the web to a remote database, which can return information as structures.
• Chemfont (Bio-Rad Laboratories) - A Windows font package that simplifies the entry of chemical equations.
• Chemical Calculator - This program calculates amounts of reagents when making solutions.
• ChemSketch (Advanced Chemistry Development) - An all-purpose chemical drawing and graphics software. Automatic calculation of molecular weight, and formula.
• ChemSymphony (Cherwell Scientific) - ChemSymphony Beans provide a platform-neutral component architecture for developing and assembling network-aware solutions in chemistry for heterogenous hardware and operating system environments run over a corporate intranet or the Internet.
• ChemWeb (Bio-Rad Laboratories) - This is a program for drawing chemical structures.
• CNS (CNSsolve) -  Crstallography & NMR System is the result of an international collaboration towards designing a flexible multi-level hierarchical approach for the most commonly used algorithms in macromolecular structure determination.  
• COLUMBUS (Hans Lischka) - A collection of programs for high-level molecular electronic calculations. It is flexible enough to perform calculations with selected reference configurations as well as standard wave functions, such as CAS, or RAS.
• Dalton Chemistry Program (Kjemisk Institutt) - A powerful quantum chemistry program for the calculation of molecular properties.
• Equilibrate (Veenstra) - This software can be used as a scientific or educational tool in biochemistry and molecular biology for quantitative analysis of molecular interactions. The program calculates equilibria and dissociation constants for interacting molecules.
• Ftrees: Feature Trees (SmithKline Beecham Pharmaceuticals R&D) - A kind of descriptor for molecular similarity and diversity analysis that uses a tree structure to represent its major chemical building blocks and conformation.
• GAMESS (Iowa State Univ.) - A program for ab initio quantum chemistry. Briefly, GAMESS can compute wave functions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available.
• Gepasi - This is for simulating systems kinetics of chemical and biochemical reactions.
• gOpenMol - A graphics interface for the OpenMol set of programs that can be used to display molecular dynamics trajectories, molecular orbitals and electron densities.
• Isoeff - Suite of programs for calculations of kinetic or equilibrium isotope effects using results of major quantum mechanical packages.
• Marvin - A java applet that is chemically intelligent and useful for editing and visualizing chemical structures on a web page.
• Mass Spectroscopy Calculator - This is a simple, but effective calculator for determining Mass Spectroscopy.
• MMCalc: Molecular Mass Calculator (Softshell) - A stand-alone application used to calculate the exact mass, or the mass percent of a formula.
• Moldy (Keith Refson) - A general-purpose molecular dynamics simulation program. It is flexible enough for the simulation calculation of atomic, ionic, and molecular systems.
• Periodic Table - This electronic periodic table serves as a supplement to learning the elemental properties.
• PHA-Pro 5. (Pharmaceuticalonline) - Program for hazard and operability, failure modes and effect analysis, and preliminary hazards analysis applications.
• PhysProps - (Pharmaceuticalonline) - Trial version of an advanced database and estimation application tool for chemical and physical properties of pure substances.
• PSI/88 (FUNET) - This program plots wave functions in 3D from semi-empirical sets.
• Swiss Pdb-Viewer (Nicolas Guex) - This program can display several molecules simultaneously. Each molecule is loaded into a individual layer and grouped according to its atomic composition and respective coordinates.
• TOXCHEM+ Version 2 (Pharmaceuticalonline) - This software will serve to estimate and report on secondary emissions from wastewater systems.
• VRML Molecular Toolbox - A collection of programs written in MATLAB 5x that allows MATLAB to generate VRML 2.0 animations.
• WINVIBES (FUNET) - Winvibes displays normal modes of vibrations of molecules.

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Molecular Biology

Genetic Analysis

• ACEDB (A Caenorhabditis Elegans Database) - A database manager that refers to a database and data concerning nematode C. elegans, or to the database software alone. Allows cross-referencing during loading.
• AMPS (G. Barton, Univ. of Oxford) - A suite of programs for multiple sequence alignment. The programs include options to incorporate non-sequence information such as secondary structures, and also implements flexible pattern matching and database scanning options.
• Analyse (Barton &Baird) - A program for the population genetic analysis of geographic variation and hybrid zones. 
• Bioperl (The Bioperl Project) - Sottware package for computational molecular biology.
• BLOCK - This program is for linkage analysis of large complex pedigrees.
• CloneIt (Institut National de la Recherche Agronomique) - A program for use in plasmid cloning to quickly find in-frame deletions, sub-cloning, and frameshifts strategies.
• CLUSTAL W (SGI) - This is a multiple sequence alignment program for biological sequences.
• Codontree (National Research Council Bari) - This program is able to determine a codon usage table for a set of protein coding genes, gene relationship on the basis of codon usage similarity, and compositional features of protein coding genes.
• createGel - Perl source code that creates a gel project out of blast results. To be used in conjunction with splitblast.
• Dang (J.M. Word, Duke Univ.) - Reads coordinates from a Protein DataBank (PDB) molecular structure file and generates a table of several useful geometric measurements for each residue or base.
• DARWIN (Data Analysis and Retrieval with Indexed Nucleotide/peptide sequences) - An interactive tool for peptide and nucleotide sequence analysis.
• DynaFit (BioKin Ltd) - Program for performing nonlinear least-squares regression of chemical kinetic, enzymatic kinetic, or ligand receptor binding data.  
• Flip (Univ. Montreal) - A Unix C program used to find and translate orfs. Flip reformats DNA sequences and produces output files that can be used by other programs such as FASTA.
• Gassoc (Mayo Foundation for Medical Education and Research) - This software makes disease and genetic marker associations using cases and their parents.
• GDA (Lewis & Zaykin) - A program for analyzing discrete genetic data.
• GENEHUNTER (MIT) - A software package that allows the very rapid extraction of complete multipoint inheritance information from pedigrees of moderate size. This information is then used in exact computation of multipoint LOD scores and in a new method of non-parametric linkage analysis.
• GeneMark (Borodovsky Group) - This program is used for gene prediction in sequences.
• Genome Inspector - This software tool detects distance associations between sequence elements.
• Glimmer (TIGR) - A system for finding genes, using interpolated Markov models to identify the coding regions and distinguish them from noncoding regions, in microbial DNA (especially the genomes of bacteria and archaea).
• Image (The Sanger Centre) - This is a package of analysis algorithms for processing gel images from restriction digest fingerprinting.
• JaMBW 1.1: Java based Molecular Biologist's Workbench (Luca I.G. TOLDO) - A collection of programs designed to exploit the most common bioinformatic operations that a molecular biologist currently has, including manipulation and analysis of DNA sequences.
• JaMBW: Java based Molecular Biologist's Workbench (EMBL-Heidelberg) - A set of tools for free access to the the mostcommon bioinformatic operations that a molecular biologist currently has.
• Kinship 1.2 (Rice Univ.) - A program to perform maximum likelihood tests of pedigree relationships between pairs of individuals in a population, It uses genotype information for single-locus, codominant genetic markers (such as DNA microsatellite loci).
• Map Manager - This program analyzes genetic mapping experimental results using backcrosses, intercrosses, or recombinant inbred strains.
• MSA (Alejandro Schaffer, Rice Univ.) - A program to do multiple sequence alignment under the sum-of-pairs criterion.
• QTL Cartographer (Statistical Genetics) - This tool maps quantitative traits using a map of molecular markers.
• RAMHA - This program is for the introduction and study of random mutagenesis in DNA sequences.
• Relatedness 5.0 (Rice Univ.) - A program that calculates average genetic relatedness among sets of  individuals defined by demographic variables, either on average or by pairs.
• RNAdraw (CABIOS) - An application that uses RNA optimal structure, basepair-probability matrix, and heat curve calculation to predict RNA structure.
• SCANPS (The Barton Group) - A local alignment method to search protein sequence databases with a query sequence or multiple alignment, and also allows all pairwise comparisons to be made between a set of sequences and can estimate the statistical significance of the alignments.
• TRANSFAC (GBF) - A database program that compiles data about gene regulatory DNA sequences and from this data programs have been developed to identify and putative promoter or enhancer structures.

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PCR

• Amplify (Univ. of Wisconsin, Genetics) - This program designs primers and simulates PCR.
• GPRIME (Bioinformatics Group, Research School of Biological Sciences) - This program helps with the design of PCR primers for an aligned group of related nucleotide sequences.
• PC-Rare (Weizmann Institute of Science) - This tool chooses specific PCR primers based on the OFD Method.
• PrimerGen (Weizmann Institute of Science) - This program searches sequences of amino acids and reverse translates them into oligonucleotide primers.
• Primers! (Apple Pi) - This program analyzes primer sequences and creates primers.
• Primer3 (Whitehead Institute for Biomedical Research) - This program is for designing primers.

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Phylogenetic Analysis

• AMP Accepted-mutation parsimony (Univ. Pennsylvania) - A data-set-derived amino acid substituted probability matrix to weight multiple, independently seeded, heuristic parsimony analysis. C source code is available.
• ANCML (Univ. British Columbia) - A program which estimates ancestor states for a continuous trait, and provides a "standard error" for the marginal distribution of each estimate.
• BIONJ - A phylogenic reconstruction algorithm, which uses an improved version of the NJ algorithm, and is well adapted when evolutionary distances are obtained from aligned sequences.
• CAFCA: Collection of APL Functions for Cladistic Analysis (Leiden Univ.) - A program which employs the methods of group-compatibility and component-compatibility to run cladistic analysis of a data matrix.
• CAIC (Univ. of Oxford) - This software implements a suite of phylogenetically comparative methods for data sets including continuous variables.
• CERVUS (Univ. of Edinburgh) - A program for likelihood-based parentage inference using codominant marker data. It can be used to calculate allele frequencies, run simulations to determine critical values of likelihood ratios and analyse parentage in populations of animals and plants.
• Cluster (Univ. of Alberta) - A clustering program that uses single and complete linkage methods to determine the heirarchial clustering for a given data set.
• COMPARE (Univ. of Oregon) - consists of several programs which analyze comparative or interspecific data while taking phylogenetic information into account.
• DELTA: DEscription Language fo TAxonomy (Biodeversity and Biological Collections Server) - A method of recording taxonomic descriptions for computer processing adopted as a standard for data exchange by the International Taxonomic Databases Working Group.
• DIPLOMO - This program is a phylogenetic workbench.
• DISTREE (Technische Universität München) - Analyzes aligned nucleotide sequences and determines the pairwise substitution rates.
• GeneTree (R.D.M. Page, Univ. of Glasgow) - A program for comparing gene and species trees.
• LVB 1.0 - This program uses unweighted parsimony to reconstruct evolution, based on a matrix of discrete characters for different objects. These characters can be aligned DNA or protein sequences, or morphological.
• MacClade (Maddison and Maddison) - The analytical strength of MacClade is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.
• MALIGN - A program for the alignment of molecular sequences based on the most parsimonious tree that can be constructed by the program algorithm.
• PAML (Ziheng Yang) - A program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood.
• PHYLIP (Univ.of Washington, Department of Genetics) - In this program, phylogenies are inferred by type of data or algorithm.
• Phylodendron - This is an application for drawing phylogenetic trees.
• PHYLTEST (Pennsylvania State Univ.) - Allows a comparison of phylogenic trees, estimation of the pairwise distances, relative rate tests, and computation of the time of divergence.
• PLATO 2.11 (Univ. of Oxford) - A program that takes sequential PHYLIP formatted DNA sequences sequences followed by their maximum likelihood phylogeny. It can detect for example, recombination, or gene conversion or convergence.
• PSeq-Gen (Department of Zoology, Univ. of Oxford) - Simulates the evolution of protein sequences along evolutionary trees following the procedures previously reported for the DNA sequence simulator Seq-Gen.
• PUZZLE 3.1 - This program reconstructs phylogenetic trees from molecular sequence data by maximum likelihood.
• QDate (Oxford) - An application for estimating the date of divergence between two pairs of sequences given that the date of divergence of the members of each pairs is known.
• Quercus (Ruth Shaw) - A program for the maximum likelihood analysis of variance of quantitative genetic data. The programs perform ML or REML on a two generation pedigree with multivariate phenotypic observations and fixed effects.
• RAPDistance - Records and fragment data can be analyzed in order to determine phylogeny.
• RASA 2.2 (Lyons-Weiler) - This is software for relative apparent synapomorphy analysis.
• Reticulate (Australian National Univ.) - A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences
• RSTCALC (Univ. of Edinburgh) - A program for performing analyses of population structure, genetic differentiation and gene flow using microsatellite data. RSTCALC calculates unbiased estimates of RST and assesses their significance using bootstrap and permutation tests.
• Seg-Gen (Department of Zoology, Univ. of Oxford) - A program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process.
• SITES (Jody Hey) - A computer program for the analysis of comparative DNA sequence data, and is primarily intended for data sets with multiple closely related sequences.
• Spectrum (Impkin Inc.) - A program designed to read in a data file comprising aligned character arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform some simple spectral analysis procedures on that data.
• SplitsTRee2 - An interactive program for analyzing and visualizing evolutionary data. Based on the split decomposition method this program takes input as a distance matrix or a set of aligned sequences and produces as output a graph that represents the evolutionary relationships between taxa.
• SPOT (Univ. of Oxford) - A program that will calculate the likelihood of a given tree topology for a set of aligned nucleotide sequences.
• Treecon (Univ. of Montreal) - This program constructs and draws evolutionary trees based on distance data.
• TreeCons (Univ. of Sydney) - A program that generates a weighted consensus tree from trees obtained by maximum likelihood analysis, and conducts the Kishino-Hasegawa test with any level of significance.
• Treemap (Taxonomy and Systematics, Univ. of Glasgow) - TreeMap is a program for comparing host and parasite trees.
• TreeTool (Univ. of Illinois, Ribosomal Database Project) - A tree plotting program that displays output in various forms and allows modification by the user in the form of labels and nodes.
• Treeview (Taxonomy and Systematics at Glasgow) - A simple program for displaying phylogenies that reads standard NEXUS and PHYLIP formatted trees.
• Treevolve v1.32 (Univ. of Oxford) - A program that will simulate the evolution of DNA sequences under a coalescent model, which allows exponential population growth, population subdivision according to an island model, migration and recombination.
• VORTEX (Bob Lacy) - This program is for population viability analysis.

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Protein Structure Prediction

• Aqua: Analyzing the QUAlity (NMR Spectroscopy Department, Bijvoet Center for Biomolecular Research) - A suite of programs for analyzing the quality of biomolecular structures that were determined via NMR spectroscopy.
• DICROPROT (PBIL) - a package of methods designed for the estimation of protein sequence secondary structure
• DomainFinder 1.0 - A program for the determination and characterization of dynamical domains in proteins.
• DOWSER (Univ. of North Carolina) - The Dowser program surveys a protein molecule's structure to locate internal cavities and assess the hydrophilicity of these cavities in terms of the energy of interaction of a water molecule with the surrounding atoms.
• FAMBE: Fast Adaptive Multigrid Boundary Element method (Univ. of North Carolina) - A program written to calculate the solvation energy of a solute molecule in a solvent. The calculation is based on the dielectric continuum model with which it is possible to calculate the free energy of polarization of the solvent by the charges of the solute molecule.
• FANTOM: Fast Newton-Raphson Torsion Angle Minimizer (National Science Foundation) - A program that calculates low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints.
• Macromolecular Geometry - A library of source code for doing a variety of calculations on protein structures and sequences.
• MC-SYM - This program determines protein and RNA 3D structures.
• MDX (MacroDox Brownian Dynamics Software) - A program for protein structure analysis.
• MODELLER (Rockefeller Univ.) - A program for homology protein structure modelling by satisfaction of spatial restraints.
• PROANAL (Alexey M. Eroshkin) - This software is used in the analysis of multiple protein alignments, and in the study of structure-function and structure-activity relationships in protein/peptide families. It may also be used to predict protein secondary structures, functionally or structurally important regions, antigenic determinants (B- and T-call epitopes) and transmembrane regions.
• PROCHECK (R. Laskowski, Univ. College London) - Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry.
• ProFIT: Protein Fold Identification Tool (The Sanger Centre) - Combines an amino acid sequence with a database of 3D structures, and has the potential to detect a fold related to the native structure of the input sequence. Free licenses are available for academic users with SGI and DEC ALPHA Workstations.
• pSAAM (A.R. Crofts, Univ. of Illinois) - Assists in analysis of protein sequences for information about secondary and tertiary structure.
• SARF2 - A program for spatial arrangement of backbone fragments in protein structures.
• SIMS: Smooth Invarient Molecular Surface (Univ. of North Carolina) - A program written to calculate the molecular surface which envelops the solvent-excluded volume of the solute molecule. The SIMS calculates a DOT presentation of the molecular surface, an array of 3D coordinates of surface elements, their normal vectors and areas.
• STAMP (The Barton Group) - A suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position.
• THREADER 2.1 - This program predicts protein tertiary structure by recognizing the correct fold from a library of selections.
• TOP - A program which compares protein structures and performs 3d database searching via the internet.
• Vienna RNA Package (Institut für theoretische Chemie) - A package for RNA secondary structure prediction and comparison consisting of a code library and several stand-alone programs for prediction and comparison.

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Sequence Analysis

• AMAS: Analyze Multiple Alignments of Protein Sequences (The Barton Group) - Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
• Antheprot 2.9 - This is a protein sequence analysis package.
• BandScan (Glyko) - Protein gel image acquisition ,documentation and analysis.
• BASS - A software program for tracking, extracting, and base calling DNA sequencing gels.
• BOXSHADE -A program that uses preprocessed multiple alignment files as input to produce printouts of aligned protein or DNA sequences.
• Chromas1.2 (Technelysium) - This program displays and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files and it allows the user to manipulate the sequences.
• CINEMA v2.02 Colour INteractive Editor for Multiple Alignments (Open Molecule Foundation) - A program that allows the visualization and manipulation of both protein and DNA sequences.
• ClustalW - ClustalW is a popular and improved multiple alignment program for DNA or proteins.
• ConsInspector (AG BIODV) - Predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. These consensus descriptions produced by the program ConsInd consist of the length of the binding site and the individual conservation of each nucleotide position within the site.
• Coresearch (AG BIODV) - This program is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences.
• Darwin - An interactive tool for peptide and nucleotide sequence analysis with a library of functions for sequence management and analysis, statistics, numerics, and graphics.
• Delila (Schneider Lab) - This software is for information analysis of protein and nucleic-acid sequences.
• DIALIGN (AG BIODV) - This is a multiple sequence alignment program that compares whole segments rather than single residues.
• Digest - This program detects restriction enzyme sites on DNA and RNA.
• DNATools (Carlsberg Laboratory) - A program package for handling and analysis of DNA and protein sequences.
• DomainFinder (Theoretical biophysics, CBM) - determination and characterization of dynamical domains in proteins.
• Dotter (The Sanger Centre) - A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis.
• Geanfammer (Park and Teichmann) - A program that summarises the whole procedure of preparing statistically and biologically more relevant protein (sequence) duplication modules of bacterial genomes.
• GelReader (NCSA) - A color imaging and analysis tool that extracts information from digitized electrophoretic gel images, allowing manipulation of lanes and bands.
• GeneDoc - GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
• Getlanes (Washington School of Medicine) - Software developed to track lanes in four-color, flouresence-based electrophoretic gel images for use in large scale sequencing projects.
• HMMER 2.1 (Washington Univ.) - A profile hidden Markov model tha can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
• HPLC-WIZARD (Bo Bergmann) - Calculates an amino acid distribution by modelling the HPLC-chromatograms by using different density funtction.
• LalnView (PBIL) - A graphical program for visualizing local alignments between two sequences for proteins and nucleic acids.
• MACAW (National Center for Biotechnology Information) - This program is a locator, analyzer, and editor for multiple sequence alignments.
• MacStripe (Molecular Motors, Univ. of York) - This is an ideal tool for anyone who wants to explore potential alpha-helical coils in the sequence of their protein.
• MatInspector2.1 (AG BIODV) - Matches in sequences of unlimited length are located by this program.
• MEME (UCSD Computer Science and Engineering Dept.) - Discovers motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and searches sequence databases using motifs using MAST.
• ModelGenerator and ModelInspector (AG BIODV) - Develops functional models for transcriptional regulatory DNA units.
• MPSA (Multiple Protein Sequence Analysis) - Software intended to protein sequence analysis.
• Multi-Cut - A java applet that gives list of buffers that are compatible with a selection of multiple restriction enzymes. Use is free via the internet.
• Mutability (Alastair Brown) - A program which takes a DNA sequence and determines how many single point mutations would result in nonsense, missense, or neutral mutations.
• MView - A tool for converting the results of a sequence database search (BLAST, FASTA, etc.) into the form of a coloured multiple alignment of hits stacked against the query.
• Nucleic Acid Structure Analysis (Sincris) - Calculates all of the rotational and translational parameters for complementary base pairs, neighboring base pairs in Cartesian and helical coordinate frames, and base to base Cartesian and helical parameters along each strand.
• Octopus (Laboratoire de Minéralogie-Cristallographie) - An interactive program designed for the rapid interpretation of BLAST, BLAST-2 and FASTA output text files. This program provides several complementary sequence analysis tools and implements a network engine allowing the user to run a BLAST-2 search on either InfoBioGen (FR), ExPASy (CH) or NCBI (USA) BLAST servers.
• pDRAW32 (AcaClone) - This program is used to draw and analyze linear and circularized DNA sequences.
• Pfam (The Sanger Centre) - A database of multiple alignments of protein domains or conserved protein regions.
• Plasmid 1.0 (Redasoft) - This program allows scientists to draw high quality sequence maps and perform DNA sequence analysis. A limited demo version is available to download.
• Plasmid Processor - In this program, plasmids are constructed for presentations involving science and education.
• Pratt (Dept. of Informatics, Univ. of Bergen) - Discovers patterns conserved in sets of unaligned protein sequences.
• Promotif (Dept. Biochemistry and Molecular Biology, Univ. College London) - Analyzes a protein coordinate file and provides details of the structural motifs in the protein.
• ProMSED2 (BioInformer) - This is for both automatic and manual DNA and protein sequence alignment, editing, comparison, and analysis.
• RepeatFinder - Perl source code that searches for DNA/protein sequence repeats.
• Restriction Map Alignment (USC Computational Biology) - This program reads restriction maps and deciphers alignments using a quantic map alignment algorithm.
• Retrak v1.5 (Washington School of Medicine) - A retracking and analysis environment for processing a large volume of gel samples.
• SAM: Sequence Alignment and Modeling System (Baskin Center for Computer Science and Engineering) - A hidden Markov modeling suite software system.
• SC rate - A Perl5 program that evaluates the accuracy of protein sequence alignment with very low sequence identity.
• SEALS (NCBI) - A software package expressly designed for large-scale research projects in bioinformatics.
• SeaView (Laboratoire de biometrie, genetique et biologie des populations) - This is a multiple sequence alignment editor.
• SeqPup (Indiana Univ.) - A biosequence sequence editor and analysis program for multiple sequence alignments and single sequence editing.
• Sequence Viewer (NCGR) - A graphical utility that is used to view DNA sequences and associated features, and it retrieves information from the Genome Sequence Data Base.
• Simple34 (Australian National Univ., Research School of Biological Sciences) - This program estimates the amount of sequence repetition in nucleotide sequences.
• SSS align - A software implementation of the Smith/Waterman best local similarity algorithm which, in addition to the traditional Dayhoff PAM scoring scheme, has the ability to use secondary structure prediction in order to align sequences which have identities as low as 15% and still identify those sequences as significant.
• webblast - A perl program that conducts NCBI blast searches by acting as a www client like Netscape or Internet Explorer. The program saves results as local files in HTML or plain text.
• WinDot - This program takes 2 DNA/RNA/Protein sequences and show their similarities and differences graphically.
• Wise2 (Sanger Center) - A software package that compares DNA sequences at the level of conceptual translation, regardless of sequencing error and introns. It can compare a single protein or a profile HMM to a genomic DNA sequence, and predict a gene structure.
• WU-BLAST (Washington Univ. School of Medicine) - This is software for gene and protein identification through sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases.
• XYLEM - A collection of tools designed enable the user to identify, extract and manipulate data from major databases such as GenBank, EMBL and PIR.

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Molecular Modeling

• AMBER (Oxford Molecular) - This is a molecular simulation program.
• ARP/wARP - A program for the refinement of protein structures that combines in an iterative manner the reciprocal space structure factor refinement with updating of the model in real space.
• CHARMM (Harvard) - An integrated macromolecular science package incorporating molecular simulation methodologies.
• ChemPen3D (Molecular Mechanics) - This is a program for building 3D molecular structures, analyzing molecular geometry and reaction energetics, and for exploring molecular mechanics. This is a fully functional 60 day trial versions of ChemPen and ChemPen3D.
• Chime  (Univ. of Massachusetts, Department of Microbiology) - This program is used to view molecular structures on Netscape.
• Cn3D (NCBI) - This 3D molecular structure viewer for data entries from Entrez, allows the rotation of structures.
• DOCK (UCSF) - DOCK addresses the problem of "docking" molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together.
• DRAGON (National Institute for Medical Research, London) - A program for protein modelling that uses distance geometry to predict the tertiary structure of a small soluble protein given its sequence, secondary structure, and possibly a set of distance restraints.
• DSSP (Kabsch and Sander) - This program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format.
• EDPDB (Florida State Univ.) - EDPDB is a FORTRAN program that simplifies the analysis of protein structure and makes it easy to extract various types of geometrical and biologically relevant information both for the molecule in isolation as well as in its crystallographic context.
• Espoir (Univ. du Maine-France) - A special purpose Reverse Monte Carlo code for ab initio crystal structure determination.
• Fantom (Sealy Center for Structural Biology, Univ. of Texas) - Calculates low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments.
• FoldIt (light) - This program visualizes and manipulates large proteins by integration of statistical analysis and 3D observations.
• FTDOCK - A program that performs rigid-body docking on two biomolecules in order to predict their correct binding geometry.
• GRASS - This tool is designed to facilitate the study of macromolecular function by mapping a number of structural, chemical, and biological properties onto various representations of molecular structure (molecular surfaces, wire frame, CPK spheres, or backbone tracing ribbons).
• GROMACS - A molecular dynamics program for multiprocessor machines. The program is a fully automated topology builder for proteins, and can conduct various simulations, as well as electrostatics and non-equilibrium molecular dynamics. It is free for non-commercial users.
• GROMOS96 - This is a general-purpose molecular dynamics simulation package.
• Insight II - A 3D graphical environment for molecular modeling.
• ISIS/Draw (MDL Information Systems) - A 2D molecular structure visualization program.
• Kinemage (D. Richardson, Duke Univ.) - A package of 2 programs (Prekins and Mage) that enables the user to create a 3D image from a PDB-format coordinate file, which then can be modified.
• LIGPLOT - A program for automatically plotting protein-ligand interactions. The interactions shown are those mediated by hydrogen bonds and by hydrophobic contacts.
• loopDloop (IUBio) - This is a tool for drawing RNA secondary structures.
• MacMolecule2 - Molecular visualization programs designed for students/teachers in chemistry, biology, biochemistry and related fields.
• MC-SYM (Univ. of Montreal) - MC-SYM searches the conformational space of RNA and generates models that are of atomic precision.
• MidasPlus - An advanced molecular modeling system that display and manipulate macromolecules such as proteins and nucleic acids.
• MINT - A graphical user interface for MODELLER that replaces the the Modeller control language.
• MOIL-View (SCI) - This program may be used to view and analyze molecular structures and dynamics.
• MOLDEN - (CAOS/CAMM Center) - A package for the visualization of molecular and electronic structure.
• Molecular Images - A package of 3 programs, Psearch, Molw and Showcase, designed for searching, viewing, analyzing, and imaging macromolecular structures from PDB files.
• MOLMOL 2.4 - This is a program for the analysis and display of molecules.
• MolScript (Avatar Software) - A program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
• MolScript (Florida State Univ.) - A program for creating molecular graphics in the form of POSTSCRIPT plot files. Possible representations are simple wire models, CPK spheres, ball-and-stick models, text labels and Jane Richardson-type schematic drawings of proteins, based on atomic coordinates in various formats. Colour, greyscale, shading and depth cueing can be applied to the various graphical objects.
• MolView - This completely interactive program can read different types of coordinate files and show various displays such as ribbon, CPK, stick, ball&stick, and surface figures.
• MOVIEMOL (Stockholm Univ. and Uppsala Univ.) - MOVIEMOL visualizes and animates molecular structures.
• MSMS (The Scripps Research Institute) - MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces. This program is written in C programming language and can be used as a standalone program or as an AVS (Advanced Visualization System) module. Binary versions of MSMS are available for SGI, Dec Alpha, HP9000 and Sun workstations.
• MSV (The Scripps Research Institute) - MSV is an OpenGL based viewer for molecular surfaces computed with MSMS.
• NAB: Nucleic Acid Builder (Scripps Research Institute) - A computer language for modelling nucleic acids, which allows description in a heirarchial fashion.
• NAMD2.0 (Theorectical Biophysics Group) - This program is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. The software is available via anonymous ftp.
• NAMOT2: Nucleic Acid MOdeling Tool (LANL) - A graphic tool to build and manipulate nucleic acid structures.
• NUCPLOT (Biomolecular Structure Modelling Group) - A program that generates schematic diagrams from 3D coordinates found in a given PDB file. The program works for single and double stranded proteins, DNA, DNA-ligand, and protein-RNA complexes.
• The O Files - A general purpose macromolecular modelling program aimed at the field of protein crystallography. It enables the scientist to model, build and display macromolecules.
• ORTEP-III (ORNL) - A thermal ellipsoid plot program for crystal structure illustrations.
• Oscail (National Univ. of Ireland, Galaway) - A software system for solving, refining and examining small molecule crystal structures.
• Phases - A package of computer programs designed to compute phase angles for diffraction data from macromolecular crystals. The package contains programs for merging and scaling of native and derivative data sets, analyzing difference statistics, computing Patterson and electron density maps, and various isomorphous replacement routines.
• PCMolecule2 - Molecular visualization programs designed for students/teachers in chemistry, biology, biochemistry and related fields.
• PovChem (Paul Thiessen) - 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.
• PREPI v0.9 - This program produces molecular representations of proteins and nucleic acids, as well providing information on secondary structure.
• Probe (J.M. Word, Duke Univ.) - Allows one to view and score atomic packing, either within or between molecules generating "contact dots" where atoms are in close contact.
• QTree - A program for generating space-filling models from PDB files. It is capable of generating worms and ball-and-stick models as well as using preprocessing filters.
• QUILT (EMBL Heidelberg) - A program to detect contiguous stretches of hydrophobic surface area on the surfaces of macromolecules.
• RasMol (Univ. of Massachusetts, Department of Microbiology) - RasMol is intended for visualization of proteins, nucleic acids, and small molecules.
• Raster3D (Florida State Univ.) - A Molecular graphics package consisting of a core program render and a number of ancillary programs (avs2ps, setup, rods, ribbon) which produce input files for rendering. Raster3D uses a fast Z-buffer algorithm to produce high quality pixel images featuring two light sources, specular highlighting, Phong shaded surfaces, and shadowing.
• RayScript (Florida State Univ.) - RayScript is a means to produce raytraced images of molecular graphics using Craig Kolb's Rayshade package and MolScript input files.
• Rayshade (Stanford Univ.) - Rayshade is an extensible system for creating ray-traced images. Its main function is to read a multi-line ASCII file describing a scene to be rendered and produce a file containing the ray traced image.
• Reduce (J.M. Word, Duke Univ.) - A program for adding hydrogens to a Protein DataBank (PDB) molecular structure file.
• ReView (Gosper, Brunel Univ.) - This program is a 4D-chemical viewer/analyzer which is capable of 3D-molecular display, animation (4D-display), and geometrical analysis.
• Ribbons - This program is used for general molecular modeling and error analysis in protein crystallography.
• RNAdraw (Ole Matzura) - This is a program for RNA secondary structure calculation and analysis.
• SIgMA: SImulations of MAcromolecules (Univ.of North Carolina) - A program for conducting energy minimization, free molecular dynamics, constrained and restrained molecular dynamics, and molecular dynamics with free-energy methods.
• Situs (W. Wriggers, Univ. California San Diego) - A program package for the docking of protein crystal structures to single-molecule, low-resolution maps from electron microscopy or small angle X-ray scattering.
• SPOCK (Texas A&M Univ.) - Molecular graphics software including several bond and atom rendering types, a complete array of backbone "worm" representations, can calculate and display molecular and accessible surfaces and color code these surfaces by properties.
• SQUID (York Univ., Dept. of Chemistry) - SQUID is a program to display/analysis/validate molecular structures, carry out MD analysis, draw 2D/3D/4D graphical representation of data, do data processing, plus a macro language.
• STING (Columbia Univ.) - A tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis.
• SURFNET v.1.4 (Roman A. Laskowski) - Generates surfaces and viod regions between surfaces from coordinate data supplied in a PDB file. It can compute: van der Waals surfaces; gaps between molecules; clefts, cavities and binding sites; 3D denisty distributions and sidechain interactions, and planes, paraboloids and boxes.
• Swiss-PdbViewer - Application that provides an interface to analyse several proteins at the same time. Amino acid mutations, H-bonds, angles and distances between atoms are easily to obtained using the graphical user interface.
• TINKER (Washington Univ. School of Medicine) - A molecular modeling software for molecular mechanics and dynamics, with some special features for polypeptides. The package includes a variety of novel algorithms such as a new distance geometry metrization method that is faster than standard algorithms, Elber's reaction path methods, Potential Smoothing and Search (PSS) methods for global optimization, Cartesian polytensor atomic multipole expansion treatment of electrostatics with explicit polarizability, Eisenberg-McLachlan ASP and MacroModel GB/SA solvation, our own truncated Newton (TNCG) local optimizer, surface areas and volumes with derivatives, a simple free energy perturbation facility, normal mode analysis, minimization in Cartesian, torsional or rigid body space, a new spherical energy cutoff method, reaction field treatment of long range electrostatics, and much more.
• TOPS (Dept. Biochemistry and Molecular Biology, Univ. College London) - Generates protein topology cartoons. Places circles and triangles depicting alpha-helices and beta-strands respectively giving a pictorial topological summary of any protein structure.
• VMD: Visual Molecular Dynamics (Theoretical Biophysics Group) - Macromolecular structures such as proteins and lipid bilayer assemblies can be visualized and analyzed by this program.
• WebLab - Combines desktop computing, validated computational chemistry methods, and the communications infrastructure offered by the World Wide Web.
• WHAT IF (EMBL) - This protein structure analysis program can be used for molecular graphics and structure verification.
• XmMol - Simple and Interactive display of macromolecular structures on any X11 server.
• XMol allows researchers to view (on any X11 or OpenGL display server) 3D molecular models produced by other software packages, and to print the molecular displays in PostScript, MAC PICT, VRML and other formats.
• XtalView (The Scripps Research Institute) - The construction of x-ray crystal structures by the fitting of molecular models into an electron density map is possible with this program.

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Numerical Analysis

• EXTNUM (NBIF) - A floating point number type that extends the dynamic range for a double type floating point number, while preserving the approximate 15 digit precision of the double as well.
• GraphPad Prism (GraphPad) - Demo version of statistical software for biostatistical analysis, curve fitting, and presentation graphics designed for the student and researcher alike.
• InStat Trial Version (GraphPad) - Demo version of statistical software specifically designed by a scientist for scientists, without the complex statistical jargon .
• MultiVariate Statistical Package (Kovach Computing Services) - Performs several types of eigenanalysis ordinations: principal components analysis (PCA), principal coordinates analysis (PCO), and correspondence/detrended correspondence analysis (CA/DCA). Only a demo version is available at this site.
• Replace (Structural Biology Program, Columbia Univ.) - A suite of programs for molecular replacement calculations.

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Software Reviews

• Alkami Biosystems PCR Reviews (Alkami Biosystems) - Reviews of a range of online and freeware PCR related tools.

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Software Repositories and Search Engines

Biotechnology Related

• Art's Biotech Resource Gateway - Link to a number of biotech sources. Software is categorized into Mac, PC and Unix formatted programs.
• BioCatalog (EMBL) - A software catalog of general interest in molecular biology and genetics. Topics include DNA, proteins, alignments, genetics, mapping, molecular evolution, molecular graphics, and databases.
• Biology Software for Alpha NT (Russell Malmberg) - A nice selection of software emphasizing MS Windows NT on a DEC Alpha.
• Bioperl Project - A collection of Perl modules for analyzing and manipulating biological sequences and computational molecular biology.
• Biosoftware Resources (George Mason Univ., Bioinformatics and Computational Biology) - This resource contains sites for tools and packages for biology research.
• CIT: Center for Information Technology (National Institutes of Health) - CIT supports NIH's research and management programs provides links to a variety of molecular biology and bioinformatics sites.
• Free and Demo Software (The Really Quite Useful MolBio Page) - A page devoted to molecular biology software for PC's.
• IUBio (Indiana Univ.) - A link to software for molecular biology and related areas.
• Jack's Molecular Biology Software Picks - This is a list of multifunctional molecular biology packages.
• Molecular Biology Shareware (Ken Peters) - A listing of shareware programs for biological sequence analysis on Windows.
• Molecular Biology Software (Academic Computing Health Sciences, Univ. of Virginia) - This page offers a small array of biotechnology related programs.
• Molecular Biophysics Software (Florida State Univ.) - Several biophysics software tools are available here for studies in molecular visualization, crystallographic data processing and protein structure analysis.
• Molecular Linux (Blip Blopps Home Page) - A listing of molecular biology software for Linux is on this site.
• NetSci's Software (Network Science) - A small link to conformational searching and analysis software.
• Neuroscience (Synergy Research Inc.) - This is a listing of sites containing packages dealing with neuroscience.
• NIH-Repositories (National Institutes of Health) - This is a listing of sites containing DNA sequence analysis software.
• NMR Software (NMR Information Server) - This page introduces a multitude of software for various NMR duties.
• Phylogenetic Analysis Computer Programs - This site contains a list of tree inference, alignment, character evolution, and tree studies.
• Phylogeny Program - A list of over 100 phylogeny software packages.
• Protein Related Software (Ezequiel Panepucci) - A list of four programs for acquiring PDB files, viewing/analyzing PDB files and calculating molar extintion coeficients.
• The Sanger Centre - A collection of shareware and freeware sequence analysis programs.
• Software Library (Genamics.com) - A software library containing a comprehensive range of freely-distributable tools for use in molecular biology and biochemistry.
• TIGR Software Tool Collection (The Institute for Genomic Research) - This has a listing of free software tools.

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General Repositories and Search Engines

• 32bit (InfoWest Global Internet Services, Inc.) - Contains 32-bit shareware programs, games and software.
• Developer.com (EarthWeb Inc.) - Contains information and resources for internet and intranet developers. It includes Gamelan, the official directory for Java, as well as news, information, tutorials, and directories for other Internet technologies including ActiveX, JavaScript, Perl, VRML.
• Download.com (CNET, Inc.) - A shareware directory from CNET.
• FAST FTP Search (FAST ASA) - An advanced file search engine for downloading of software, computer games, images, and audio files.
• Filemine (CMP Media Inc.) - Contains shareware, freeware, commercial demos and games. Also includes reviews, collections of related products and featured titles.
• Filez (Zco Inc.) - A Search engine that scans file servers worldwide by entering file name or category for downloading.
• Freeware32.com - A collection of 32-bit freeware and shareware with ratings.
• Genetic Analysis Software (Rockefeller Univ.) - This list is an alphabetical compilation of software dealing with genetic linkage analysis, marker mapping, and pedigree drawing.
• Graphics and Data Analysis software (S. Baum) - Contains links to software designed for graphing 3-D data, number crunching tasks (manipulation of large and multi-dimensional matrices) and software for storing various types of data in standard and/or compressed format.
• HENSA: The Higher Education National Software Archives (JISC) - Maintains copies of electronic archives and provides access to a wide range of software and other material which is available free of charge from the UK Higher Education community. It provides software for the Unix operating system, PC's and microcomputers.
• Java Code Libraries (Univ. of Toronto) - A collection of a wide variety of Java code repositories. It contains a collection of Java applets, utilities, and programmer tools.
• Jumbo - Searchable database of freeware and shareware for OS/2 and other platforms.
• Mac on the Net - A collection of Internet connection software for the Macintosh.
• Mathematics Software Repositories (Univ. of Arizona) - A list of Mathematical and statistical software repositories sites for OS/2 and other operating systems.
• MCS Software (Argonne Nat. Laboratory) - A collection of software applications for chemistry, protein structure, vortex dynamics, astrophysics, climate modeling, mathematics and logic, CFD, and reservoir simulation
• NERDC: Northeast Regional Data Center (NERDC Information Services) - A collection of Internet software.
• Netlib - Netlib Repository is a collection of free mathematical software, papers, and databases of interest to the numerical, scientific computing, and other communities.
• OAK Software Repository (Oakland Univ.) - A collection of computer software and information to Internet users free of charge.
• OS/2 Shareware Web & BBS (Norloff Computer Corp.) - A collection of OS/2 shareware, freeware and public domain programs and information.
• Rocketdownload.com (Share|Tech, Inc.) - Contains popular shareware and freeware programs for downloading. Reviews, descriptions and screenshots are also available.
• Sharepaper (Zco Inc.) - Direct download links to popular shareware, demos and trial software titles. It also includes reviews, information, and screen shots.
• Shareware.com (CNET, Inc.) - A searchable shareware database of software files from CNET. It includes freeware, shareware, demos, fixes, patches and upgrades from software archives and computer vendor sites on the Internet.
• Shareware Library (Industry.net, Inc.) - Shareware for Windows software, Dos and OS/2 utilities, artificial intelligence, motion control & robotics, circuit design, engineering tools, finite element analysis, spectrum analysis, accounting, math, science & physics, networking, C programming, visual basic for Windows, plotting utilities, games, graphs, and weather forecasting.
• Shareware Shop (Biondo Software) - Contains software archives for Windows, giveaways, and reviews.
• Softseek - Contains shareware, freeware, and software reviews.
• SunSite: Sun Information and Technology Exchange (Univ. of North Carolina) - A Sun Microsystems sponsored program at key universities around the world. It maintains a large archive of public domain software available via ftp for sun equipment users.
• TUCOWS - A collection of Internet Software providing different mirror sites for downloads.
• UMich Mac Archive (Univ. of Michigan) - A collection of Macintosh files available for downloading.
• Winfiles.com (Jenesys LLC) - Provides a collection of 32-bit shareware, Drivers, tips, explanations, and information about Microsoft Windows operating systems.
• Winsite (The WinSite Group, Inc) - Contains software archive for Windows shareware and trialware.
• ZDNet Software Library (ZDNet) - Offers Internet shareware and demo downloads.

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Support Tools and Utilities

Graphics

• BioBrowser (Proteometrics) - Browser for viewing BIOML files. Requires Microsoft Internet Explorer version 4.01 or later.   
• Graphic Converter - This tool takes image files and convert them to GIF files.
• Graphics Workshop (Alchemy Mindworks Inc.) - This workshop allows an individual to view, manipulate, and manage graphics.
• Kinemage - This is a display program to view and explore kinemages.
• Lview Pro - Lview Pro is an image viewer and editor with JPEG support.
• NcView 1.65 (Climate Research Division) - A visual browser for netCDF-format files.
• NIH Image (National Institute of Mental Health) - Acquires, displays, edits, enhances, analyzes and animates images. It can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles.
• OSIRIS (ExPASy) - A general medical image manipulation and analysis software designed for physicians and non computer-oriented users.
• PDBViewer (ExPASy) - Swiss-PdbViewer can load and display several molecules simultaneously.
• PiXCL Tools 4.14 (VYSOR Integration Inc.) - This is a 2D graphics, image display and processing language toolkit and EXE builder.
• Scion Image (Scion Corporation) - Can acquire, display, edit, enhance, analyze and animate images. It can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles.
• ShadyBox - This drawing program enables boxing and shading of regular and irregular shaped segments of aligned multiple sequences.
• TN-Image (NIH) - A scientific analysis program that can create, edit, and produce color print images. Useful for analysing gel, MRI, and X-ray images.
• WIT (Logical Vision) - Image processing software that supports several options including image resizing and rotation, color-space and object manipulation, and image aquisitions.  

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Graphing and Statistical Analysis

• Axum (MathSoft, Inc.) - A technical data analysis and graphing program which provides 2D and 3D graphs.
• CrossGraphs (Belmont Research Inc.) - A software tool that helps the user visualize, understand, and report complex, multidimensional data in analysis databases and data warehouses.
• Dynafit (BioKin Ltd.) - Dynafit makes nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data.
• gnuplot - A command-line driven interactive function plotting utility that handles both curves (2 dimensions) and surfaces (3 dimensions).
• Kalkulator (J. Andrzej Wrotniak) - This is a versatile and powerful 'calculator' for scientists.
• NLREG: NonLinear REGression analysis program - A program that performs linear and nonlinear regression analysis and curve fitting. NLREG can handle linear, polynomial, exponential, logistic, periodic, and general nonlinear functions.
• SAAM (NCI/FCRDC) - Developed primarily for biological systems and more specifically for kinetic and dynamic models specified as compartmental models, the program is of general utility.

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Miscellaneous

• Adobe Acrobat Reader (Adobe Systems Inc.) - This tool reads Adobe Acrobat (.pdf) files.
• BackTrack (StrandWare) - Software package combining databases, advanced label design, flexible report generating software, and developing tools for tracking applications.  
• Beyond Bio 101 (Howard Hughes Medical Institute) - This book describes the changes taking place in how American college students learn biology.
• BIOSTAT B (Protein Chemistry Laboratory, Univ. of Aarhus) - Control and collection software for the BioStat B fermentor.
• DosLynx v0.8 - This is a distributed hypertext browser with some WWW capabilities.
• GAGEtrak Version 3.5 (CyberMetrics Corp.) - Demo version of a comprehensive calibration management system for scheduling calibrations, tracking calibration performance history and conducting Gage R&R Studies.
• Genemachine (J. Ryan, NHGRI)- Runs GRAIL, MZEF, GENSCAN, FGENES, Sputnik, RepeatMasker and BLAST and prints the output in ASN.1 format.
• JUMBO (Peter Murray-Rust) - A pure Java application for the demonstration of XML and CML.
• MLWorks (Harlequin) - MLWorks is an integrated development environment with a set of graphical tools that takes advantage of SML's sophisticated module system and polymorphic type system to provide many of the benefits of object-oriented languages with the added security of a static type system.
• Pmb Binary File Format Utilities ( H. Sauro) - Utilities which enable metabolic/chemical kinetic models to be read and exported to and from different kinetic simulators.  
• PubCrawler (Genetics Dept., Trinity College) - Searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters specified by the user. It can keep scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests.
• vExplorer - This is a metabolic control analysis tool.
• WS FTP - This is a 32 bit graphical FTP client.
• X-PLOR (Yale) - This program has files for protein and DNA/RNA X-ray crystallography and Solution NNR spectroscopy.

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Typefonts

• Internet Type Foundry Index (Chris MacGregor) - A source of type related information .

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Web Authoring

• AOL Press - This is a web authoring tool for creating web sites.
• Gemstone (Eamonn Sullivan) - Gemstone provides a crash course on writing HTML documents.
• HomeSite (Allaire Corp.) - This is a useful editing tool for maintaining and creating web sites.
• HotMetal (SoftQuad Inc.) - This is a free HTML writing software from SoftQuad.
• Netmind free services (NetMind Services, Inc.) - This site has a collection of free Web utilities.
• Spyglass HTML Validator (Spyglass) - This is a tool for checking documents against HTML markup language.

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X Windows

• MI/X (MicroImages, Inc.) - This X Window package provides multitasking , remote execution, and the display of graphics on one X terminal that were generated somewhere else in a network. This is a free X-Server which is available for the Windows 95, NT and Macintosh platforms.
• X-WinPro (Labtam Finland Ltd.) - A 32-bit software package that transforms a PC into an X Windows workstation. The X Window System, TCP/IP, TFTP, and Telnet software are provided in the package. X-WinPro is only operational for 30 minutes per run for an unlimited number of runs. It is available for the Windows 95, NT and 3.xx platforms.
• X-Win32 (StarNet Communications Corp.) - X-Win32 is X Window System server for Microsoft Windows 3.1, Windows for Workgroups 3.11, 95, 98 and NT 4.0. X-Win32 Version 4.1 (for Windows 95, 98 and Windows NT 4.0) and X-Win32 Version 3.4.1 (for Windows 3.1 and Windows for Workgroups 3.11) demo enables the user to evaluate X-Win32 for only a period of two hours at a time.

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Last Updated: October 28, 1999