Software

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

The Bio Log
DNA Baser sequence aligner is a software package providing automatic DNA sequence assembly functions, contig editing functions and chromatogram viewing and editing.
http://www.thebiolog.com

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

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

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/

DNA Chromatogram Explorer
Freeware program that can automatically view, trim and convert all chromatogram files (SCF, ABI, AB1, AB) in the current folder.
http://www.dnabaser.com/download/chromatogram-explorer/index.html

Free FASTA/MultiFASTA converter tool
This tool will look for all FASTA files in the specified folder and will merge their content in a single file, generating a standard or custom MultiFASTA file. Just download the program and double click to run it. It does not need additional software/add-ons/Java or VBRun packages to run.
http://www.dnabaser.com/download/FASTA-Converter/index.html

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/

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/

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/

Pegasys
Open source software for executing and integrating analyses of biological sequences. Includes documentation and installation instructions.
http://www.bioinformatics.ubc.ca/pegasys/

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/

RNA Baser Sequence Assembly Software
Software tool specialized in processing rRNA sequences and optimized for early integration of sequence and metadata. The metadata will stay attached to the primary sequence information throughout the complete workflow of sequence analysis, until final submission.
http://www.rnabaser.com/

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

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/

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

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