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/

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

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

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-
- http://www.dnabaser.com/download/FASTA-Converter/index.html

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

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

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/

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

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/

Gene Expression Open Source System
- Open source database and analysis package used to archive and analyze expression data from gene chip experiments. Includes microarray center workflow management, and researcher tools to analyze final data.
- https://biostat.virginia.edu/geoss/site/

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/

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/

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

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/

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

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

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/

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

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

STRand
- Open-source Windows program to automate or speed up the analysis of DNA fragment length polymorphism samples run on ABI3730, 3700 and 377 sequencers. Instructions for use and program download available.
- http://www.vgl.ucdavis.edu/STRand

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/

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

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/