Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
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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.
[Glyko] Protein gel image acquisition, documentation, and analysis.
[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 and Molecular Analysis Section
[NIH] BIMAS offers many bioinformatics tools, including DNA sequence analysis, a mirror of GeneCards, genetic linkage analysis, and more. A catalog of linkage analysis software is also provided.
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
Computational Services at EMBL
[EMBL] Ties together sequence search and retrieval, alignment, data submission, comparison and prediction into one site. Also available are tools for structure verification and related software.
EBI ftp Server
The EBI ftp server provides a comprehensive archive of databases and software in the field of
[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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Genetics Software Archive
[Indiana State Univ.] Annotated links to downloadable genetics and molecular biology software for the PC.
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.
Links to molbio software
[Erasmus University] Annotated links to downloadable molecular biology software.
Contains numerous, annotated links to Linux software for chemistry. Also included is whether the software is free, shareware, or commercial.
Molecular Biology Software
[Hospital for Sick Children, Toronto] Perl source code programs for DNA sequence analysis and other bioinformatics related applications.
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.
[University of Washington] A list of over 100 phylogeny software packages.
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.
Protein Modelling Software
[National University of Singapore] Well-annotated links to software for protein modelling programs and their online manuals.
[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.
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[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.