CloneMap provides a complete solution for fast and easy plasmid map drawing,restriction site mapping, and virtural cloning. High-quality plasmid maps can be created with or without DNA sequences. Map features can be added by restriction site searching, feature table parsing, or easy, interactive manual entry. Restriction sites can be displayed on the map using predefined enzyme filters, or reported as text files summarizing sites together with DNA sequences. Common DNA sequence manipulations such as translation, open reading frame identification and display, and sequence conversion are provided. Free form graphic drawing objects, floating text, and Windows metafile can be added to the map to enhance map presentation. Map fragments can be inserted or deleted to generate related maps, with concomitant changes in the underlying DNA sequences.
Submitted: Sep 27, 2000
Molecular Weight Calculator  
The Molecular Weight Calculator calculates a molecule's molecular weight (or formula weight), and the molecule's percent composition, displaying the results for up to seven compounds simultaneously. The program is available in Windows 9x/NT, Windows 3.x, and Dos versions. The Windows 9x/NT and 3.x versions contain the added features of a Mole/Mass Converter and a Formula Finder, plus easy exchange of information to/from other Windows applications.
Submitted: Dec 23, 2000
The group of Prof. Berend Smit has developped BIGMAC, which is a general-purpose Configurational Bias Monte Carlo (CBMC) code. You can download a version of this code for grand-canonical and gibbs ensemble simulations of simple linear alkanes (approximately 7.6 MB).
Submitted: Jan 06, 2001
CNMR & HNMR Viewers  
ACD/SpecViewer freeware for viewing NMR, > MS, IR and UV-Vis EXPERIMENTAL data in standard formats
Submitted: Oct 24, 2000
Lasergene99 is the complete sequence analysis system for Windows and Macintosh. Unlike any other system, Lasergene99 delivers: A full suite of sequence analysis tools, The Speed, power and sophistication to handle any size project, Internet connectivity with integrated BLAST searching, Support for ABI®, AB1®, SCF, Genbank, FASTA, GCG®, MacVector® and more formats.
Submitted: Sep 20, 2000
Free Windows software for the detection of recombination in aligned sequences. Performs sliding window distance/similarity, bootscanning, and informative sites analysis.
Submitted: Mar 11, 2003
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
Submitted: Sep 27, 2000
NJplot is a tree drawing program 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: Sep 19, 2000
Image is a package of analysis algorithms for processing gel images from restriction digest fingerprinting experiments.
Submitted: Sep 05, 2000
Divide-and-Conquer Multiple Sequence Alignment  
Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences.
Submitted: Sep 26, 2000
Oxford Molecular  
Oxford Molecular Group is a worldwide supplier of integrated molecular design software and collaborative research services, for use by companies and academic institutions in the fields of pharmaceutical and biotechnology research.
Submitted: Dec 23, 2000
Redasoft Visual Cloning 2000 is a major upgrade to Plasmid 1.1 that integrates molecular biology research with the Internet. New features include enhanced graphics, expanded restriction analysis, Open Reading Frames search, primer design, subsequence search, a sequence viewer and extensive web integration.
Submitted: Sep 20, 2000
A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.
Submitted: Sep 07, 2000
A software company developing modern, intelligent, user-friendly programs for molecular biologists.
Submitted: Sep 30, 2000
IUBio Archive for Biology  
This is an archive of biology data and software, established in 1989 to promote public access to freely available information, primarily in the field of molecular biology.
Submitted: Sep 15, 2000
This is the right place for you if you are looking for a molecule viewer for LINUX! The most important advantages of KMovisto are: KMovisto imports GAUSSIAN 94 or 98 files without conversions. KMovisto imports and exports XYZ files. KMovisto exports POV-Ray files for rendering high quality presentations. KMovisto exports VRML files for 3D presentations in the world wide web. KMovisto is really easy to use. KMovisto is free software, that means you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.
Submitted: Dec 22, 2000
MatInd and MatInspector  
MatInd is a simple but powerful method to derive a matrix description of a consensus from a number of short sequences on which the definition of a IUPAC code would be based. A large library (~280 entries) of predefined matrix descriptions for protein binding sites exists and has been tested for accuracy and suitability. Information about the transcription factors connected to these matrices can be retrieved from the TRANSFAC database. MatInspector is a second software tool that utilizes this library of matrix descriptions to locate matches in sequences of unlimited length.
Submitted: Sep 30, 2000
The Sequence Alignment and Modeling system (SAM) is a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. The model states can be viewed as representing the sequence of columns in a multiple sequence alignment, with provisions for arbitrary position-dependent insertions and deletions in each sequence. The models are trained on a family of protein or nucleic acid sequences using an expectation-maximization algorithm and a variety of algorithmic heuristics. A trained model can then be used to both generate multiple alignments and search databases for new members of the family.
Submitted: Sep 23, 2000
DIALIGN is an alignment program that relies on comparison of whole segments of the sequences instead of comparison of single residues. Pairwise as well as multiple alignments are constructed from gapfree pairs of equal length segments. These segment pairs are called `diagonals'.
Submitted: Sep 07, 2000
The program system MOLGEN is devoted to the computation of all structural formulae (=connectivity isomers) that correspond to a given molecular formula, with (optional) further conditions (e.g. substructures). MOLGEN arose from the idea to provide an efficient and portable tool for molecular structure elucidation in both chemical industry, research and education.
Submitted: Nov 24, 2000
PERCH is a software package for processing and analyzing 1D NMR spectral data. In addition to the common processing tools PERCH offers very powerful routines for modern spectral analysis and the quantification of NMR data. These include a proton NMR shift and coupling prediction based on the 3D molecular structure and a fairly automated verification of a structure-spectrum correlation based on a sophisticated iterative algorithm using integral transforms.
Submitted: Oct 08, 2000
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
Submitted: Sep 09, 2000
RdLength calculates the Radiation Length of a single molecule based on its empirical formula. The program also displays the formula needed to calculate the Radiation Length of a multi-molecular material.
Submitted: Dec 22, 2000
VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.
Submitted: Dec 22, 2000
ANTHEPROT (ANalyze THE PROTeins) is a package to make protein sequence analysis such as alignment, secondary structure predictions, sites & function detection, physico-chemical profiles, homology search and 3D display of protein structures.
Submitted: Sep 19, 2000
Bass is Unix-based software for tracking, extracting, and base calling DNA sequencing gels. It can handle the data file formats produced by the ABI 373 and 377 machines, as well as the wide format produced by the 373 with the Washington University/Sanger Center ROM Patch.
Submitted: Sep 06, 2000
Molecular Biology Software: Comprehensive Genomic Sequence Analysis Packages/Suites, Genetic Mapping Tools/Utilities, Linkage Analysis Tools, Primer Selection Tools, Sequence Similarity, DB Search Tools, Sequence Database Access Tools, Sequence Analysis Tools, and more.
Submitted: Oct 08, 2000
Software package for computational molecular biology.
Submitted: Sep 05, 2000
CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. For specific families of proteins additional characteristics are used to weight the alignment.
Submitted: Nov 05, 2000
Chromas is a Windows application which displays and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create.
Submitted: Sep 06, 2000
A tool for the prediction of protein binding sites in nucleic acids.
Submitted: Sep 07, 2000
DEJAVU Package  
DEJAVU is a program that will help you find out if the fold of (a part of) your protein occurs in any other protein in the Protein Data Bank (PDB). The program compares the spatial orientation of (a subset of) the secondary-structure elements (SSEs) in your protein with that of a database of SSEs which is derived from the PDB (and updated once or twice a year).
Submitted: Dec 23, 2000
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.
Submitted: Sep 30, 2000
Automatically generates schematic diagrams of protein-ligand interactions for a given PDB file.
Submitted: Sep 11, 2000
MacPlasmap and CloneMap  
Software solutions for DNA and protein analyses, plasmid map drawing, and electronic virtual cloning.
Submitted: Sep 30, 2000
This program is used to draw and analyze linear and circularized DNA sequences.
Submitted: Sep 09, 2000
Automated crystallographic structure solution for MIR, SAD, and MAD.
Submitted: Dec 10, 2000
A Numerical Hartree-Fock Program for Diatomic Molecules.
Submitted: Jan 06, 2001
Pretty Printing and Shading of Multiple-Alignment files.
Submitted: Sep 06, 2000
The PASCAL program BOXSHADE, intended for shading multiple aligned sequence files.
Submitted: Sep 19, 2000
LalnView is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences.
Submitted: Sep 09, 2000
MacStripe is the ideal tool for anyone who wants to explore potential alpha-helical coiled coils in the sequence of their protein. With a full Macintosh interface, the results of analyses (raw data or publication quality plots) can easily be exported to other software.
Submitted: Sep 09, 2000
Fast and sensitive tools for detection of consensus matches in nucleotide sequence data.
Submitted: Sep 09, 2000
ModelGenerator and ModelInspector  
ModelGenerator is a new method to develop functional models for transcriptional regulatory DNA units (e.g. promoters). The method requires a training set of at least 10 sequences containing the regulatory unit to be modelled and a simple initial model (e.g. two characteristic transcription factor binding sites and their sequential order). ModelInspector utilizes these models to scan sequences for new regulatory units matching the model. ModelInspector is also able to carry out database searches with these models.
Submitted: Sep 09, 2000
ProFIT (Protein Fold Identification Tool) combines an aminoacid sequence with a database of 3D structures, and has the potential to detect a fold related to the native structure of the input sequence.
Submitted: Sep 06, 2000
REPLACE is a suite of programs for molecular replacement calculations. It currently consists of two major programs, GLRF for rotation function calculations and TF for translation function calculations. In addition, a small program (ANGCAL) is a convenient tool for conversions between angles and matrices.
Submitted: Oct 15, 2000
SciVision, founded in 1992, is a division of Academic Press, San Diego, California, based in Burlington, Massachusetts. Since its inception, the company has focused on development, marketing, and support of high-quality, high performance, desktop scientific application and molecular modeling software products. A combination of database information and computational tools to process and analyze such information is the "hallmark" feature of SciVision's line of desktop products.
Submitted: Dec 23, 2000
A Program to Calculate the Steric Size of Molecules about a Point in terms of their Cone Angles and Solid Angles, as well as their total Volumes and Projected Areas.
Submitted: Dec 22, 2000
The SURFNET program generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file.
Submitted: Sep 15, 2000
Textco, Inc.  
Developer of high quality software for molecular biologists since 1984.
Submitted: Jan 19, 2001
ALP is a Microsoft Windows application designed to analyse microsatellite DNA fragments separated on an Automated Laser Fluorescence sequencer.
Submitted: Sep 19, 2000
Amplify is a Macintosh program for simulating and testing polymerase chain reactions (PCRs). It can also be used as a tool for designing primers by evaluating candidates.
Submitted: Sep 05, 2000
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. Cn3D runs on Windows, MacOS, and Unix. Cn3D simultaneously displays structure, sequence, and alignment.
Submitted: Sep 16, 2000
COMBOSA3D is used to color a three-dimensional representation of a protein according to the results of a sequence alignment. The program accepts a group of pre-aligned sequences in FASTA format (one of the sequences must have a solved three-dimensional structure), and it uses the alignment information to highlight conserved residues on the molecule.
Submitted: Jan 06, 2001
A tuple search algorithm for identification of consensus elements in unaligned nucleic acid sequences.
Submitted: Sep 07, 2000
Software for Information Analysis of Protein and Nucleic-acid Sequences.
Submitted: Sep 07, 2000
A GNU/Linux-based system, called the DEgenerate Oligonucleotide Design & Analysis System (DEODAS), for designing and electronically analyzing consensus-degenerate oligonucleotides is being developed by integrating published software tools Clustalw, CODEHOP, and EMBOSS.
Submitted: Jan 06, 2001
DNA Stacks Software Package  
Doug Eernisse of the California State University, Fullerton ( has constructed DNA Stacks version 1.2, a Macintosh HyperCard stack that can carry out a variety of analyses on DNA sequences. It does not do phylogenies itself. It has an alignment editor, and can carry out various kinds of translation, and codon bias analysis.
Submitted: Oct 15, 2000
DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins.
Submitted: Sep 06, 2000
EpoDB( Erythropoiesis database) is a database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites.
Submitted: Oct 15, 2000
ESSA is an integrated and interactive computer tool for analysing RNA secondary structure.
Submitted: Sep 30, 2000
The purpose of the GERM program is to develop three-dimensional atom-based models of previously uncharacterized receptor sites, starting from a small structure-activity series of active and inactive compounds (3 or more structures).
Submitted: Jan 06, 2001
gff2ps is a program for visualizing annotations of genomic sequences. The program takes as input the annotated features on a genomic sequence in GFF format, and produces a visual output in PostScript. It can be used in a very simple way, because it assumes that the GFF file itself carries enough formatting information, but it also allows through a number of options and/or a configuration file, for a great degree of customization.
Submitted: Sep 30, 2000
MacClade is a computer program for phylogenetic analysis. It is not intended as a stand-alone tool to infer phylogeny (although it complements programs like PAUP nicely in this regard). Its analytical strength 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.
Submitted: Sep 05, 2000
Molecular Networks  
Molecular Networks provides a variety of software tools for solving a host of problems from these areas. Care has been taken to develop methods that can be run on inexpensive workstations or personal computers and, nevertheless, be applicable to large datasets of molecules.
Submitted: Dec 23, 2000
Molecular Programming LLC.  
Creators of fine DNA and protein sequence analysis software for the molecular biology research community.
Submitted: Oct 31, 2000
MORASS uses a full hybrid matrix eigenvalue/eigenvector solution to the Bloch equations to derive cross-relaxation rates and interproton distances. MORASS analyzes 2D NMR NOESY data from oligonucleotides and proteins to evaluate cross-relaxation rates from which interproton distances are obtained.
Submitted: Oct 24, 2000
PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) is a threading-based protein structure prediction system. PROSPECT is designed particularly for the recognization of the fold template whose sequence has insignificant homology to the target sequence.
Submitted: Nov 23, 2000
QTL Cartographer  
A suite of programs to map quantitative traits using a map of molecular markers.
Submitted: Sep 05, 2000
SAM (System for Assembling Markers) takes an input a file of clones and their marker content. The output is a graphical display which shows the order of the markers and the alignment of the clones to the markers. A solution can be saved in a file which can subsequently be loaded back into SAM.
Submitted: Jan 06, 2001
SAMBA is a 128 processor array for speeding up the comparison of biological sequences. The hardware implements a parameterized version of the Smith and Waterman algorithm allowing the computation of local or global alignments with or without gap penalty.
Submitted: Oct 17, 2000
Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. It is capable of handling simple submissions which contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, segmented sets of DNA, or phylogenetic and population studies.
Submitted: Sep 30, 2000
Software Sharing Archive  
This is an archive for a mailing list/discussion group devoted to issues of software sharing in genomic research that is maintained at the MIT/Whitehead Institute Center for Genome Research.
Submitted: Oct 08, 2000
SPSOFT provides high-performance and high-throughput sequence analisys software solutions on general-purpose computer systems.
Submitted: Oct 31, 2000
PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch.
Submitted: Sep 06, 2000
TreeMap is an experimental program for comparing host and parasite trees. It is available for both Windows and Apple Macs.
Submitted: Sep 06, 2000
Program Package for ab initio Electronic Structure Calculations.
Submitted: Oct 18, 2000
Wise2 is package that is focused on comparing DNA sequences at the level of its conceptual translation, regardless of sequencing error and introns. This really is a rewrite of the old wisetools package, which I wrote about 3 years ago.
Submitted: Sep 30, 2000
The PDB through Microsoft Windows, or WPDB for short, is a Microsoft Windows 3.1 Windows95 and Windows NT (client and server) based program to interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above.
Submitted: Oct 08, 2000

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