Web Directory

» Alice Software
   Database system to build and publish synonymised checklists of species. Species descriptions include pre-established fields and detailed descriptions employing any number of user-defined fields.
   http://www.alicesoftware.com/

» Alternative Splice Site Predictor
   ASSP predicts putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons.
   http://es.embnet.org/~mwang/assp.html

» Binary State Pattern Clustering
   BSPC is a method for pattern discovery in gene expression microarray data, that makes use of a perspective that interprets gene activity as being in two or more discrete functional states.
   http://compbio.charite.de/index.php/BSPC.html

» BioConstructor Molecular Cloning Software
   BioConstructor is a bioinformatics solution focussing on molecular cloning. Runs on Windows, Mac OS X, Linux.
   http://www.bioconstructor.com

» Broad Institute Genetics Software
   Offers a wide range of software for genome sequence analysis, genetic variation, linkage analysis, expression analysis, and PCR primer selection.
   http://www.broad.mit.edu/tools/software.html

» CREME: Cis-REgulatory Module Explorer
   Identifies modules of putative transcription factor binding sites that are specific to promoters of co-expressed human genes. Provides a resource for decoding microarray experiments.
   http://creme.dcode.org/

» CellProfiler
   Open source image analysis software designed for biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
   http://www.cellprofiler.org

» CounterTrace II DNA Sequencing
   Software and reagent for improving the quality and read length of DNA sequence traces collected on the ABI 3730 DNA sequencer.
   http://www.nucleics.com/DNA_sequencing_tools/DNA-sequencing-software-countertrace.html

» GENtle
   GPL software for viewing and editing DNA and amino acid sequences. Integrated alignment, PCR, BLAST searches, and shared databases. Windows version is available for download (English and German).
   http://gentle.magnusmanske.de/

» Gene Array Analyzer Software
   Software for the efficient management, analysis and visualization of large amounts of gene expression data.
   http://www.medinfopoli.polimi.it/GAAS/

» Gene Expression Open Source System
   Open source database and analysis package used to store and analyze gene expression data. Includes microarray center workflow management, and researcher tools to analyze final data.
   http://va-genex.sourceforge.net/

» GeneSifter
   Web-based microarray analysis system that combines data management and analytical functions with integrated, current gene annotation from public databases. Product overview in pdf format.
   http://www.genesifter.net/web/

» Genetic Linkage Analysis
   Offers links and other resources for genetic analysis software from the Rockefeller University.
   http://linkage.rockefeller.edu/

» Genetic Network Maps as Java Applets
   Genetic networks controlling development in Sea Urchin represented as Java applets. Formal scheme. Molecular interactions modelled as Petri Net.
   http://www.bio.davidson.edu/courses/genomics/mirror/Urchin/u0maps.htm

» Genex Open Source Gene Expression Database
   Genex is an open source database for storing, processing, and analyzing gene expression microarray data.It is intended for local installation by medium sized laboratories with some system administration support. No activity since 2003.
   http://genex.sourceforge.net/

» Hands on Genetics
   Instructional software for basic genetics, such as DNA, PCR, Mendel, Hardy-Weinberg, meiosis and computer simulations. Freeware for Mac and Windows.
   http://www.handsongenetics.com

» HyPhy: Hypothesis Testing Using Phylogenies
   Free multiplatform software package intended to perform maximum likelihood analyses of genetic sequence data.
   http://www.hyphy.org

» MapMakerDrawer
   Program that draws chromosome maps (as EMF files) using the output of MapMaker EXP. Delphi source code is freely available upon request. The software is available under the MIT licence.
   http://www.emboss.co.nz/products.php?pid=2

» MuStaR Sequence Variant Database Software
   Designed to create a database of mutation loci, to make this information available to as many people as possible. No longer being maintained.
   http://www.hgu.mrc.ac.uk/Softdata/Mustar/

» Mutation Explorer
   Software to automatically detect mutations from DNA sequence data, including homozygous, heterozygous, insertion and deletion.
   http://www.softgenetics.com/mutationExplorer.html

» OpenBiomind
   OpenBiomind is an open source toolkit for analysis of gene expression, SNP and other biological datasets using advanced machine learning and pattern mining techniques, and includes traditional clustering, hybrid clustering, and other techniques.
   http://code.google.com/p/openbiomind/

» PeakTrace Basecaller
   Software for base and quality scoring ABI DNA sequencing traces. Works with all ABI DNA sequencers including the ABI 377, ABI 310, ABI 3700, ABI 3100, ABI 3130 and ABI 3730.
   https://www.nucleics.com/peaktrace/

» Phenosystems
   Software company developing user friendly tools for the molecular genetics community. Provides details of products, R and D collaborations and news.
   http://www.phenosystems.com

» Progeny Software
   Supply pedigree drawing and genetic data management software for genetic research with a built-in customizable relational database.
   http://www.progenygenetics.com

» PyMoods
   A software application for visualizing genomic data. Can be used to analyze and display relations between complete genomes, genomic fragments, proteins, ESTs, full length cDNAs, and gene expression data.
   http://allometra.com/

» Random Genetic Optimization
   Genetic algorithms are a new approach to modeling based on the evolution theory in biology and use concepts such as population, descendant, parents, mutations, chromosomes, genes, etc.
   http://www.genoptim.narod.ru/ENG/

» STRand
   Open-source program, provided by Davis' Veterinary Genetics Lab at the University of California, to automate or speed up the analysis of DNA fragment length polymorphism samples.
   http://www.vgl.ucdavis.edu/informatics/strand.php

» Seqool
   Free Windows software tool for the analysis of DNA and RNA sequences. It includes several sequence statistics and a comprehensive set of signal search methods.
   http://www.biossc.de/seqool/index.html

» Synopsis
   Commercial Windows software for visualization and annotation of genomic data.
   http://www.ananomouse.com/products/synopsis.asp

» The Sequence Manipulation Suite
   The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching purposes, and for program and algorithm testing.
   http://bioinformatics.org/sms2/