Computational & Web Resources
Cell & Molecular Biology
Genetics & Evolution
Life Sciences (Other)
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Mircobiology Software. 101science.com is a science web directory, tutor, and research learning center.
A. C. R. Martin Bioinfo Site
Downloadable Java software for bioinformatics, including a Needleman-Wunsch program and a protein structural least-squares fit program.
[EBI] (G.J. Barton) "ALSCRIPT takes a multiple sequence alignment in AMPS block-file format and a set of formatting commands and produces a PostScript file that may be printed on a PostScript laser printer, or viewed using a PostScript previewer."
AMAS: Analyze Multiple Alignments of Protein Sequences
[EBI] Allows the identification of functional residues by comparison of sub-groups of sequences arranged on a tree.
[EBI] A suite of programs for multiple protein 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.
Analytical Biostatistics Section
[NIH] The ABS offers downloadable software and servers in the areas of sequence analysis, protein structure prediction, ligand binding, and gene expression.
Aneda, formerly Edinburgh Biocomputing Systems, develops software tools for biologists including the MPSRCH(tm) suite of Smith-Waterman sequence analysis programs which run on general purpose hardware at BLAST-like speeds.
[Institute of Biology and Chemistry of Proteins] (ANalyse THE PROTeins) This free software application integrates into a single package most of the methods designed for
protein sequence analysis. Methods include: Sequence information,
Sequence edition, dot matrix plot,
FASTA/BLAST, sites/signatures detection, physico-chemical profiles, secondary structure prediction, helical wheel projections, multiple alignments,
prediction of signal peptide and cleavage sites, 3D display of molecules, amphiphilicity, and
Artemis sequence viewer
[The Sanger Centre, U. K.] The Artemis sequence viewer and annotation tool allows visualization of DNA sequence features and sequence analysis, including six-frame translation. Artemis can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Written in Java, Artemis is available for UNIX, Macintosh or MS Windows.
B Molecular Modeling
[Scripps Institute] Formerly called Biomer, this Java applet builds molecular models to order. Designate components like DNA bases and amino acids to assemble into one molecule. The program also offers functions for energy minimization and molecular dynamics.
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[Glyko] Protein gel image acquisition, documentation, and analysis.
[Whitehead Institute for Biomedical Research] A software program for tracking, extracting, and base calling DNA sequencing gels.
[EMBL] The Biocatalog is a software directory of general interest
in molecular biology and genetics. The full database is downloadable (text file).
Biocompare, The Consumer Guide for the Life Scientist, offers information such as technical specs, prices, and peer reviews of life science products and services (including Bioinformatics). Biocompare also offers information
about the latest technologies in the life science community and provides scientists with a list of companies that offer discounts for setting up new laboratories.
Bioinformatics & Pattern Discovery
[IBM] Information and bioinformatics related servers developed at IBM. Services include sequence pattern analysis, gene expression analysis, and multiple sequence alignment. Servers may be used online, or the code may be downloaded.
[Aalborg University] This Blocking Gibbs Sampling for Pedigree (Linkage) Analysis in Very Large Pedigrees program is for linkage analysis of large complex pedigrees.
[EMBnet.ch+] A program that uses preprocessed multiple alignment files as input to produce printouts of aligned protein or DNA sequences.
CBIL bioWidgets for Java
[University of Pennsylvania] The bioWidgets toolkit is a collection of Java Beans (tm) used for development of graphics applications and/or applets in the
[Univ. of Massachusetts, Department of Microbiology] This program is used to view molecular structures on Netscape.
[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.
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[Univ. College London] Cinema allows the building of alignments interactively; either by using a free-format Cut and Paste facility to import a protein or DNA sequence, or by adding sequences directly from the OWL composite database. Alternatively, alignments may be loaded from the PRINTS fingerprint database and again may be customized by the addition of user-defined or OWL sequences.
[SGI] This is a multiple sequence alignment program for biological sequences.
[EBI] ClustalW is a popular and improved multiple alignment program for DNA or proteins.
Computational Biology and Informatics Laboratory
[University of Pennsylvania] Multiple bioinformatics related tools and databases. The site also includes information about related degree programs and UPenn.
Computational Biology Tools
[Cornell Theory Center] This site provides several downloadable programs for analyzing protein sequences for predictions in the areas of folding, structure determination, energetics, and dynamics. It also is home to the LOOPP program (Learning, Observing and Outputting Protein Patterns), a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure.
[GSF] 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.
[GSF] This program is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences.
Cornell Theory Center
[Advance Cluster Computing Consortium] A high-performance computing and interdisciplinary research center. This site provides information about the center, resources like software and training, and research information.
DARWIN Molecular Sequence Analysis
[CBRG] An interactive tool for peptide and nucleotide sequence analysis with a library of functions for sequence management and analysis, statistics, numerics, and graphics.
DDL - Drug Design Laboratory
[Milan University, Italy] This site presents downloadable programs for drug design, including molecular dynamics for solvated molecules, program Predator to predict secondary structure of proteins, and molecular orbital calculations.
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[Decodon] Analyze protein 2-dimensional gels. Compare protein spots on two gels with image analysis techniques. Download free demo version or purchase full program.
[National Cancer Institute] This software is for information analysis of protein and nucleic-acid sequences.
[GSF] DIALIGN is a novel program for multiple alignment. It 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.
[DNAssist] A DNA sequence editing and analysis application.
[Carlsberg Laboratory] Software for handling and analysis of nucleotide and protein sequences.
This downloadable package also has special functions for EST and SAGE handling and analysis.
[K. Hinsen] (Centre National de la Recherche Scientifique) A program for the determination and characterization of dynamical domains in proteins.
[Karolinska Institutet, Center for Genomics Research] Compares two related sequences and finds matches, creating a dotplot. Accompanying the dotplot are excellent statistics and user-friendly adjustment of thresholds. Download the program to run on Unix. A server version is available at http://www.hgmp.mrc.ac.uk/Registered/Option/dotter.html for registered users.
DSSP Source Code
[CMBI] "The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB)."
EBI ftp Server
The EBI ftp server provides a comprehensive archive of databases and software in the field of
[Arizona Research Laboratories] FAKtory is a software environment for supporting DNA sequencing
projects. FAKtory runs on machines configured with the UNIX operating
system. It is called FAKtory because it employs our FAKII Fragment
Assembly Kernel that is a C-library of routines
incorporating our best algorithms for solving the shotgun assembly
problem. FAKtory is highly configurable and can perform fragment
clipping, prescreening, and tagging functions, shotgun assembly with or
without constraints, and sequence finishing. An extensible input/output
mechanism permits FAKtory to be inserted into any informatics
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FASTA Program ftp
[University of Virginia] The latest versions of the FASTA sequence similarity search programs are available for download at this site.
[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.
[Compugen] An algorithm for searching protein databases with DNA queries, based on Smith-Waterman. FramePlus independently and simultaneously models frame shifts and codon gaps.
FSSP ftp Site
[EBI] The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB).
[University of Split, Croatia] A free molecular visualization program intended to ease some of the hardships non-computer scientists may have with RasMol's command line interface.
[Medical Research Council, UK] A program for the analysis of bacterial genomes.
[NCSA] A color imaging and analysis tool that extracts information from digitized electrophoretic gel images, allowing manipulation of lanes and bands.
[GenPak Inc.] Compare whole genomes at the DNA sequence level, looking for identical stretches of bases. Program creates a dotplot, sequence list, and statistics. Download a working version free, or pay for the expensive version.
[Pittsburgh Supercomputing Center] GeneDoc does sequence alignment editing and shading, as well as secondary structure shading and super family group support.
[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.
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[J. Ryan, NHGRI] Runs GRAIL, MZEF, GENSCAN, FGENES, Sputnik, RepeatMasker, and BLAST; and prints the output in ASN.1 format.
[Georgia Tech] This program is used for gene prediction in sequences. "The GeneMark program relies upon an Inhomogeneous Markov Model approach combined with training datasets to predict genes. Along with predicting genes, it can use RBS models to predict RBS sites and predict frameshifts."
Genetics Software Archive
[Indiana State Univ.] Annotated links to downloadable genetics and molecular biology software for the PC.
[GSF] This software tool detects distance associations between sequence elements.
[Washington School of Medicine] Software developed to track lanes in four-color, flourescence-based, electrophoretic gel images for use in large scale sequencing projects.
[TIGR] "Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria and archaea. Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA."
[Columbia University] "GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties."
[Washington Univ., St. Louis] A protein sequence analysis tool that profiles hidden Markov models (profile HMMs) that can be used to do sensitive database searching using statistical descriptions of a sequence family's consensus.
[Net-ID, Inc.] A general purpose hidden Markov model (HMM) simulator for biological sequence analysis.
[Molecular Software] Molecular visualization software with an easy to use GUI.
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[Stanford University] (Luciano Brocchieri) A program for the multiple alignment of protein sequences.
JamBW 1.1: Java Based Molecular Biologist's Workbench
[EMBL] 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.
[University of Cambridge] JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features.
[D. Richardson, Duke Univ.] A package of 2 programs, Prekins and Mage, that enables the user to create a 3-D image from a PDB-format coordinate file, which then can be modified.
[PBIL] A graphical program for visualizing local alignments between two sequences for proteins and nucleic acids.
Links to molbio software
[Erasmus University] Annotated links to downloadable molecular biology software.
Linux for Chemists
A virtual library of Linux software links in the areas of chemistry, biochemistry, computational biology and bioinformatics.
MACAW ftp Site
[NCBI] "MACAW is a program for locating, analyzing, and editing blocks of localized sequence similarity among multiple seqences and linking them into a composite multiple alignment."
[Univ. of York] MacStripe will explore potential alpha-helical coiled coils in the sequence of a protein.
MatInd and MatInspector2.1
[GSF] Tools for detection of consensus matches in nucleotide sequence data .
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[Nathan Kopp] [Annotation pending]
[San Diego Supercomputing Center] "The MICE application provides high quality, interactive visualization of molecular scenes. Written in JavaTM and Java3D, MICE is designed according to the Java philosophy of “write once, run anywhere.” Portable and web-deliverable, the MICE application enables users to not only view molecular scenes on their own computer, but to distribute these scenes and interact with other users anywhere on the internet."
The Microbiology Network
Molecular Biology and Biotechnology File Archive.
These files include standard shareware
programs of interest to the microbiologist,
programs designed by individual investigators,
text files in specialized interest, and
demonstration programs supplied by vendors.
ModelGenerator & ModelInspector
[GSF] Methods for generation and recognition of models for regulatory regions in DNA sequences.
[Rockefeller Univ.] A program for homology protein structure modelling by satisfaction of spatial restraints.
Molecular Biology Software
[Hospital for Sick Children, Toronto] Perl source code programs for DNA sequence analysis and other bioinformatics related applications.
Molecular Structure Computer Programs
[University of Lunds] Several program packages dealing with molecular structure analysis and NMR data analysis.
This is a program for the analysis and display of molecules.
[University of Florida] "A PDB to POV file converter and molecular visualization tool for MS Windows."
[Avatar Software AB] "MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations."
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[NPSA] "Multiple Protein Sequence Analysis is a stand-alone software package for protein sequence analysis with a high integration level and Web
client/server capabilities. It provides many methods and tools, which are integrated into an interactive graphical user
[Rice Univ.] A program to do multiple sequence alignment under the sum-of-parts criterion.
MSA: Multiple Sequence Alignment
[Washington Univ.] Reads a file containing several protein sequences and attempts to produce a multiple alignment of these sequences, which it will write to standard output. MSA uses the algorithm of Altshcul et al., Gupta et al. or ClustalW.
[National Institute for Medical Research] Converts the results of BLAST, FASTA, and other sequence database searches to a coloured multiple alignment of hits stacked against the query.
[S. Hubbard & 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 residual accessiblities for both proteins and nucleic acids.
NCBI FTP Site
Provides FTP access to NCBI tools and databases, including BLAST, Cn3D, Sequin, the NCBI Toolbox, BLAST databases, GenBank, and many collections of contributed molecular biology data.
Noncovalent Bond Finder
[University of Massachusetts] [Annotation pending]
Nucleic Acid Structure Analysis
[International Union of Crystallography] This program 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.
[Laboratoire de Minéralogie-Cristallographie] (Patrick Durand) Octopus is an interactive program designed for the rapid interpretation of BLAST, BLAST-2,
and FASTA output text files. It provides an easy-to-use graphical
user interface for both experienced and inexperienced users with
sequence comparison analysis based on the widely-used BLAST series of softwares.
[Murdoch University] The Online Researchers Bioinformatics Interface Tools project was established to implement an easy to use web based
interface for registered members of the Murdoch Bioinformatics Research
Group (MBRG). The system provides interfaces to the server side programs BLAST, Repeat Masker, and ClustalW; while still providing a framework for many other programs to be added to the interface in
the future. This is a downloaded Java program.
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[University of Cambridge] A program for infering phylogeny of globular proteins.
Patched POV-ray Version
[Biozentrum, University of Basel] A patch to the current (3.1g) POV-ray source which adds the object smooth_color_triangle to a mesh object. This allows for triangles with individual colors for each vertex, which are interpolated during rendering.
pDRAW32 DNA analysis software
[AcaClone Software] A free, feature-rich, DNA software application. Capabilities include annotation, cloning, sequence editing, enzyme selection, graphical output, and more. According to the author, "Actually pDRAW32 is not freeware - rather it is "beerware." This means that if you like the program you are encouraged to buy me a beer if you should meet me at a scientific meeting. You are mostly at risk of that if you attend conferences on yeast genetics."
Pfam ftp Site
[Washington University, St. Louis] The ftp site for downloading the Pfam protein domain database and the associated tools.
PHD Secondary Structure Software ftp Site
[Columbia University] [Annotation pending]
Phred Phrap Consed System Home Page
[University of Washington] This set of widely used programs does the following. Phred reads DNA sequencer trace data, calls bases, and assigns quality
values to the bases. Phrap assembles shotgun DNA sequence data. Consed is graphical tool for editing Phrap assemblies. SWAT and CROSS_MATCH do sequence similarity searches.
[University of Washington] A list of over 100 phylogeny software packages.
Pratt - A Pattern Discovery Tool
[University of Bergen] Discovers patterns conserved in sets of unaligned protein sequences.
[University of California, San Francisco] A service for protein secondary structure and class prediction.
[EMBL] Protein secondary structure prediction from a single sequence or a set of sequences.
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[EMBL] Permits the user to submit a sequence for prediction. Links to other pages for multiple sequence alignment, prediction of secondary structure, prediction of solvent accessibility, prediction of transmembrane helices, prediction of topology for transmembrane proteins, fold recognition by prediction-based threading, and evaluation of secondary structure prediction accuracy.
PROBE ftp Site
[NCBI] PROBE is a tool for extraction of multiple alignments from a sequence database.
Programs for biosequence analysis
This page contains example implementations in Java of some algorithms for pairwise alignment (including the Needleman-Wunsch algorithm), hidden Markov models (HMMs), and phylogenetic trees. Some are available as Java applets you can run from this page.
[Univ. College London] Analyzes a protein coordinate file and provides details of the structural motifs in the protein.
[University College London] "Promotif analyzes a protein coordinate file and provides details of the structural motifs in the protein."
ProMSED2 and ViSEd1.1 ftp Site
[Indiana University] At this ftp site, users may download ProMSED2 and ViSEd1.1 which are both muliple sequence alignment editors for the Windows platform.
Protein Analysis & Modelling Software
[University College London] Publicly available bioinformatics software. Most of these programs are for the analysis of protein sequence and structure.
Protein Modeling Software and Services
[University of California, San Francisco] Access to protein modeling programs produced in the Fred Cohen Laboratory.
Protein Modelling Software
[National University of Singapore] Well-annotated links to software for protein modelling programs and their online manuals.
[Centre de Biochimie Structurale] This new software assigns secondary structure elements in protein structures from the Ca trace (Labesse G., Colloc'h N., Pothier J. and
Mornon J.-P., CABIOS, vol 13., no. 3, pages 291-295).
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RasMol 2.7.1 and 2.7.2
[Bernstein+Sons] New versions of RasMol, for molecular display and manipulation, with new manual, languages other than English.
RasMol, Chime & Protein Explorer
[University of Massachusetts] [Annotation pending]
[TIGR] RBSfinder is a
Perl script that
algorithm to find ribosome binding
sites for genes in bacterial and
archaeal genomes. It is normally run as
a post-processor to the Glimmer gene
finder or to other prokaryotic gene
Restriction Map Alignment
[USC Computational Biology] This program reads restriction maps and deciphers alignments using a quantic map alignment algorithm.
[Washington Univ. - St. Louis] A retracking and analysis environment for processing a large volume of gel samples.
[Gosper, Brunel Univ.] This program is a 4-D chemical viewer/analyzer, which is capable of 3-D molecular display, animation, and geometrical analysis.
[Centre National de la Recherche Scientifique] Sequence Alignment by Genetic Algorithm. SAGA is optimally designed for the alignment of less than 20 sequences and less than 400 residues.
An automated multiple intermediate sequence search used to detect distant sequence
homology. Intermediate sequence search is a strategy for recognizing distant homologues using transitive sequences. This
method is useful when similarity between two remotely homologous sequences can not be detected by normal sequence
[MRC Laboratory of Molecular Biology] A Perl5 program that evaluates the accuracy of protein sequence alignments with very low sequence identity.
[EBI] 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.
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[NCBI] A software package expressly designed for large-scale research projects in bioinformatics. Its goal is "to facilitate large-scale semi-automatic sequence analysis projects, leveraging human intelligence by simplifying laborious tasks, without taking human judgment out of the loop."
[Genetique et Biologie des Populations] This is a multiple sequence alignment editor.
See in 3-D
[NCBI] (Cn3D) "Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service."
[Indiana Univ.] A biosequence sequence editor and analysis program for multiple sequence alignments and single sequence editing.
[Australian National Univ.] This program estimates the amount of local sequence repetition in nucleotide sequences.
[TIGR] A list of links to very useful molecular biology and bioinformatics-related freeware. The list includes programs for DNA sequencing and sequence analysis, genomic searches, and microarray image processing.
[Univ. of Edinburgh] 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.
[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.
[EBI] "STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only
multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments."
STING Server and Software
[Weizmann Institute] "STING is a WWW 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."
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[EMBL] STRIDE provides knowledge-based protein secondary structure assignment from atomic coordinates.
[ExPASy] Provides an interface allowing analysis of several proteins at the same time by superimposing them in order to deduce structural alignments and compare their active sites or any other relevant parts.
[University of Tuebingen] "TeXshade is an alignment shading software completely written in TeX/LaTeX which can process multiple sequence alignments in the .MSF and the .ALN file format. It provides in addition to common shading algorithms special shading modes featuring functional aspects, e.g. charge or hydropathy, and a plenitude of commands for handling shading colors, text styles, labels, legends and even allows the user to define completely new shading modes."
[Future Skill software] This is a metabolic control analysis tool.
[University of Illinois at Urbana-Champaign] Visual Molecular Display "is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Unix or Windows, is distributed free of charge, and includes source code."
[Hospital for Sick Children, Toronto] 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.
[National Human Genome Research Institute] NHGRI WebBLAST is a suite of downloadable software tools to aid in viewing and organizing genetic sequencing data.
[CMBI] This protein structure analysis program can be used for molecular graphics and structure verification.
[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.
[San Diego Supercomputing Center] "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. "
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[Washington Univ., St. Louis] This is software for gene and protein identification through sensitive, selective, and rapid similarity searches of protein and nucleotide sequence databases.
[Yale] This program has files for protein and DNA/RNA X-ray crystallography and solution NNR spectroscopy.
[University of Manitoba] A collection of tools designed enable the user to identify, extract, and manipulate data from major databases such as GenBank, EMBL and PIR.
[University of Graz] "YASARA is an interactive real-time molecular dynamics program, covering various topics in the field of molecular modeling, protein fold calculation (based on NMR data), tertiary structure prediction, protein / DNA docking, and parallel macromolecular dynamics."