Directory of Software Resources

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This category is for sites about stand-alone computer programs which process biological information such as genetic sequences.

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Resources in This Category

• ADF MAGE-ML

  http://adfconverter.sourceforge.net/
  Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).

• AnnHyb

  http://bioinformatics.org/annhyb/
  Free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.

• ARCiB -- Accessible Retired Computers in Biology

  http://arcib.dowling.edu/
  NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structural biology, for software packages on various platforms.

• BioAfrica.net: Bioinformatics Software and Tools

  http://www.bioafrica.net/bioinformaticstools.html
  Bioinformatics software applications and tools developed by researchers. All the tools are open-source and freely available online.

• Biochemfusion: Enabling Biochemformatics

  http://www.biochemfusion.com/
  Software for working with post-translationally or chemically modified peptides and proteins including proteins as both sequences and chemical structures.

• BioEdit

  http://www.mbio.ncsu.edu/BioEdit/bioedit.html
  Free Windows biological sequence alignment editor.

• BioMAJ

  http://biomaj.genouest.org/
  Workflow engine dedicated to bio-data synchronization and processing.

• Biomax BioXM Knowledge Management Environment

  http://www.biomax.com/products/bioxm.php
  Project-centered, distributed software platform that provides a central inventory of information and knowledge. Users create, manage and visualize scientific models as an extendible network of interrelated concepts.

• biOpen

  http://www.lightwave-scientific.com/Resources/biOpen.pdf
  Commercial Mac OS X sequence analysis and structure visualization software.

• CentiBiN: Centralities in Biological Networks

  http://centibin.ipk-gatersleben.de/
  Application for the calculation and visualization of centralities for biological networks.

• CodonCode Corporation

  http://www.codoncode.com/
  Offers CodonCode Aligner, a DNA sequence assembly, sequence alignment, contig editing and mutation detection software for Windows and Mac OS X.

• Cytoscape

  http://www.cytoscape.org/
  Open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. It is also a general platform for complex network analysis and visualization.

• Darwin

  http://cbrg.inf.ethz.ch/Darwin/index.html
  An interactive tool for peptide and nucleotide sequence analysis.

• DNA Baser Sequence Assembler

  http://www.dnabaser.com/
  DNA sequence assembly software package capable of fully automated sequence assembly.

• DNAMAN

  http://www.lynnon.com/
  Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.

• DNPTrapper

  http://dnptrapper.sourceforge.net/
  A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.

• EMBOSS

  http://emboss.sourceforge.net/
  The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG.

• FASTA

  http://www.ebi.ac.uk/Tools/fasta/
  William Pearson's package for fast sequence comparison tools.

• Geneious

  http://www.geneious.com/
  This research software is designed for biologists and not computer scientists. It combines all the major DNA and protein sequence analysis tools into one software solution.

• Generic Model Organism Database Construction Set

  http://gmod.org/
  Collection of interoperable open source software components for visualizing, annotation and managing data.

• GeneRunner

  http://www.generunner.net/
  A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product.

• GeneSifter

  http://www.genesifter.net/
  Provides complete systems for data-intensive genetic analysis applications like microarrays and next gen sequencing-based transcription. From Geospiza, Seattle, USA.

• Genespotter

  http://www.genespotter.de/
  Commercial Windows software for analyzing biochip image data.

• Genome-tools Web Interface

  http://sourceforge.net/projects/genome-tools/
  Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.

• Gints

  http://gints.free.fr/english/eng_whatsAbout.htm
  Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.

• HapEvolution

  http://www.med.mun.ca/PTRG/What-We-Do/Research/PTRG-Research/HapEvolution.aspx
  Java application which finds gene-gene interactions (multi chromosome) using SNP with interactive visualization.

• INCA - INteractive Codon Analysis

  http://www.bioinfo-hr.org/inca
  Windows software that computes and charts codon and amino acid frequencies in whole genomes. Produces fully customizable scatter plots with the possibility to export graphics or text files for further analysis. Free for academic users.

• JAligner

  http://jaligner.sourceforge.net/
  Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.

• limmaGUI

  http://bioinf.wehi.edu.au/limmaGUI/index.html
  A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.

• MaGe (Magnifying Genomes) - Microbial genome Annotation System

  http://www.genoscope.cns.fr/agc/mage/
  The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes.

• MARBL

  http://www.cs.uni.edu/~okane/source/MARBL/proc1.html
  MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.

• MedScan

  http://www.ariadnegenomics.com/products/medscan.html
  Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.

• MIRA

  http://chevreux.org/projects_mira.html
  A sequence assembly suite with SNP detection for "hard" projects.

• pDRAW32

  http://www.acaclone.com/
  Freeware DNA cloning, analysis and visualization software.

• Phrap/Consed

  http://www.phrap.org/
  DNA sequence assembler and finishing tools from the UW Genome Center.

• PhyloSort

  http://phylosort.sourceforge.net/
  A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.

• Premier Biosoft International

  http://www.premierbiosoft.com/
  Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, plasmid maps, gateway cloning, protein interaction network and functional genomics.

• RGBG Analyzer

  http://www.immunokin.com/
  Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 and XP.

• Seqtools

  http://www.seqtools.dk/
  Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.

• Sequence Analysis

  http://www.informagen.com/SA/
  A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.

• SeWeR

  http://bioinformatics.org/sewer/
  An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.

• Sockeye

  http://www.bcgsc.ca/gc/bomge/sockeye/
  3D visualisation platform for Comparative Genomics visualisation.

• Tandem Repeats Finder

  http://tandem.bu.edu/trf/trf.html
  Locates and displays tandem repeats in DNA sequences.

• The ARB Project

  http://www.arb-home.de/
  A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.

• Unipro UGENE: Integrated Bioinformatics Tools

  http://ugene.unipro.ru/
  Free cross-platform bioinformatics software package for DNA and protein sequence analysis.

• XDigitize

  http://www.molgen.mpg.de/~xdigitise/
  A Linux/Unix visualization software system for evaluation of hybridisation experiments.

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