Online Services 174
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| | Software - Computing, Healthcare, Business 650
 EMBOSSEMBOSS
 
The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG.
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ADF MAGE-MLADF MAGE-ML
 Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
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AlmaKnowledgeServerAlmaKnowledgeServer
 Text mining tool for genomics, proteomics platforms and drug discovery.
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AnnHybAnnHyb
 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.
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APBioKnoppixAPBioKnoppix
 Knoppix based bioinformatics software tools. Bootable from CD.
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The ARB ProjectThe ARB Project
 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.
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ARCiB -- Accessible Retired Computers in BiologyARCiB -- Accessible Retired Computers in Biology
 NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.
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Biochemfusion: Enabling BiochemformaticsBiochemfusion: Enabling Biochemformatics
 Software for working with post-translationally or chemically modified peptides and proteins including proteins as both sequences and chemical structures.
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BioEditBioEdit
 Free Windows biological sequence alignment editor.
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Bioinformatics Software ToolsBioinformatics Software Tools
 Provides access to a number of tools including biological databases, sequence allignment, analysis and manipulation tools and structural analysis tools. Also provides a glossary of bioinformatics terms.
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Bioinformatics Tools in HaskellBioinformatics Tools in Haskell
 A bioinformatics library implemented in Haskell, including various utilities based on it.
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Biological Concept Diagram EditorBiological Concept Diagram Editor
 A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes.
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BioMAJBioMAJ
 Workflow engine dedicated to bio-data synchronization and processing.
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Biomax BioXM Knowledge Management EnvironmentBiomax BioXM Knowledge Management Environment
 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.
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biOpenbiOpen
 Commercial Mac OS X sequence analysis and structure visualization software. [PDF]
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CentiBiN: Centralities in Biological NetworksCentiBiN: Centralities in Biological Networks
 Application for the calculation and visualization of centralities for biological networks.
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DarwinDarwin
 An interactive tool for peptide and nucleotide sequence analysis.
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DNA CounterDNA Counter
 Small free Windows program to calculate nucleotides frequencies in DNA sequences.
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DNAMANDNAMAN
 Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
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DNPTrapperDNPTrapper
 A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
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Expression ProfilerExpression Profiler
 An open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics, machine-learning algorithms and visualization.
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FASTAFASTA
 William Pearson's package for fast sequence comparison tools.
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FASTA ConverterFASTA Converter
 Free Windows tool for merging multiple FASTA files into a single FASTA file.
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FriendFriend
 An integrated multiple structure visualization and multiple sequence alignment application. Available for Windows, Linux.
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GDEGDE
 An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.
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GeneiousGeneious
 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.
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GeneRunnerGeneRunner
 A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product.
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GenespotterGenespotter
 Commercial Windows software for analyzing biochip image data.
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Genome-tools Web InterfaceGenome-tools Web Interface
 Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.
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GintsGints
 Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
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GoCoreGoCore
 GoCore is a free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
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gsuffixgsuffix
 C-language implementations of generalized suffix-based algorithms useful for searching for string patterns in sets of input strings and is released under the terms of the LGPL license.
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HMMERHMMER
 Profiles protein sequence data using hidden Markov models of a statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
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INCA - INteractive Codon AnalysisINCA - INteractive Codon Analysis
 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.
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JAlignerJAligner
 Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
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JSTRINGJSTRING
 Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format.
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KoriBlastKoriBlast
 Commercial graphical software for Blast searches.
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limmaGUIlimmaGUI
 A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
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MAFFTMAFFT
 Multiple sequence alignment program for linux and other unix-like operating systems. Offers a range of multiple alignment strategies.
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MaGe (Magnifying Genomes) - Microbial genome Annotation SystemMaGe (Magnifying Genomes) - Microbial genome Annotation System
 The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes.
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MARBLMARBL
 MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.
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MauveMauve
 Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features.
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MedScanMedScan
 Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
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MELTINGMELTING
 Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.
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Meta-MEMEMeta-MEME
 Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
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MIRAMIRA
 A sequence assembly suite with SNP detection for "hard" projects.
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msa.cgb.ki.semsa.cgb.ki.se
 Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa.
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Nano+Bio-CentreNano+Bio-Centre
 Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.
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NCBI BLASTNCBI BLAST
 BLAST (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
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NEXML: Phylogenetic Data in xmlNEXML: Phylogenetic Data in xml
 Exchange standard for representing phylogenetic data, inspired by the commonly used NEXUS format but more robust and easier to process.
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pDRAW32pDRAW32
 Freeware DNA cloning, analysis and visualization software.
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Phrap/ConsedPhrap/Consed
 DNA sequence assembler and finishing tools from the UW Genome Center.
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PHREDPHRED
 A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users.
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PhyloSortPhyloSort
 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.
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Premier Biosoft InternationalPremier Biosoft International
 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.
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RGBG AnalyzerRGBG Analyzer
 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.
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SeqtoolsSeqtools
 Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
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Sequence AnalysisSequence Analysis
 A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
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SeWeRSeWeR
 An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
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SfoldSfold
 Predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use.
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SockeyeSockeye
 3D visualisation platform for Comparative Genomics visualisation.
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STRAPSTRAP
 Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation.
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STRINGSTRING
 Search for Tandem Repeats IN Genomes. Includes C source code and examples.
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sys-bio.orgsys-bio.org
 Software for simulating metabolic, signal and genetic networks. Home of SBW, Jarnac, JDesigner and winSCAMP.
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Tandem Repeats FinderTandem Repeats Finder
 Locates and displays tandem repeats in DNA sequences.
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Unipro UGENE: Integrated Bioinformatics ToolsUnipro UGENE: Integrated Bioinformatics Tools
 Free cross-platform bioinformatics software package for DNA and protein sequence analysis.
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WU-BLASTWU-BLAST
 The Washington University improved version of BLAST. Free for academic users.
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XDigitizeXDigitize
 A Linux/Unix visualization software system for evaluation of hybridisation experiments.
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