Software Bioinformatics Biology


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








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EMBOSS* - The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG.

  • The ARB Project - A free sequence database application for Unix. It biology includes a biology sequence editor, several sequence aligners, phylogeny biology reconstruction tools, probe/primer search biology and generation, genome annotation biology and visualization. In addition to the biology integrated user-interface
  • Genome-tools Web Interface - Genome-tools provides flexible tools and a simple API biology for genomic biology sequence processing on genomes published in biology the standard Genbank format.
  • Darwin - An interactive tool for peptide and nucleotide sequence analysis.
  • Tandem Repeats Finder - Locates and displays tandem repeats in DNA sequences.
  • DNA Baser - Sequence assembly software package including a free tool biology for merging multiple FASTA files into a single biology FASTA file.
  • Geneious - This research software is designed for biologists and biology not computer bioinformatics scientists. It combines all the major biology DNA and protein sequence bioinformatics analysis tools into one biology software solution.
  • DNPTrapper - A Linux assembly editing and visualization tool specifically software designed for bioinformatics manual analysis and finishing of repeated software regions.
  • JSTRING - Java program for searching Tandem Repeats (TR) in software a DNA bioinformatics sequence. It shows the results also software in a graphical format.
  • MedScan - Commercial Windows natural language processing software for the biology automated extraction of biological data from scientific literature.
  • Premier Biosoft International - Developers of software for real time PCR primer design, TaqMan, software molecular beacons, SYBR green, FRET, DNA microarray analysis, software restriction cloning, plasmid maps, gateway cloning, protein interaction network software and functional genomics.
  • FASTA - William Pearson's package for fast sequence comparison tools.
  • gsuffix - C-language implementations of generalized suffix-based algorithms useful for software searching for string patterns in sets of input software strings and is released under the terms of software the LGPL license.
  • sys-bio.org - Software for simulating metabolic, signal and genetic networks. Home of biology SBW, Jarnac, JDesigner and winSCAMP.
  • Phrap/Consed - DNA sequence assembler and finishing tools from the biology UW Genome Center.
  • GoCore - GoCore is a free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
  • Biomax BioXM Knowledge Management Environment - Project-centered, distributed software platform that provides a central bioinformatics inventory of bioinformatics information and knowledge. Users create, manage bioinformatics and visualize scientific models bioinformatics as an extendible network bioinformatics of interrelated concepts.
  • Biological Concept Diagram Editor - A tool designed for efficient knowledge and data biology capture from electronic resources for sharing, mining and biology presentation purposes.
  • MARBL - MARBL is a free (GPL) system to index bioinformatics the text portions of GenBank and associated NLM bioinformatics abstracts. Based on Mumps and the MDH.
  • GeneSifter - Provides complete systems for data-intensive genetic analysis applications software like microarrays biology and next gen sequencing-based transcription. software From Geospiza, Seattle, USA.
  • Unipro UGENE: Integrated Bioinformatics Tools - Free cross-platform bioinformatics software package for DNA and bioinformatics protein sequence analysis.
  • JAligner - Java implementation of the dynamic programming algorithm Smith-Waterman bioinformatics for biological local pairwise sequence alignment.
  • BioMAJ - Workflow engine dedicated to bio-data synchronization and processing.
  • ARCiB -- Accessible Retired Computers in Biology - NSF supported project to make old computers accessible software to new software in bioinformatics. Provides transitional and software supplemental support, especially in structural biology, for software software packages on various platforms.
  • KoriBlast - Commercial graphical software for Blast searches.
  • STRING - Search for Tandem Repeats IN Genomes. Includes C biology source code bioinformatics and examples.
  • APBioKnoppix - Knoppix based bioinformatics software tools. Bootable from CD.
  • Genespotter - Commercial Windows software for analyzing biochip image data.
  • NEXML: Phylogenetic Data in xml - Exchange standard for representing phylogenetic data, inspired by bioinformatics the commonly used NEXUS format but more robust bioinformatics and easier to process.
  • Biochemfusion: Enabling Biochemformatics - Software for working with post-translationally or chemically modified software peptides and proteins including proteins as both sequences software and chemical structures.
  • XDigitize - A Linux/Unix visualization software system for evaluation of biology hybridisation experiments.
  • MaGe (Magnifying Genomes) - Microbial genome Annotation System - The MaGe system offers a set of graphical software interfaces which allow biologist to perform relevant expert software annotation of microbial genomes.
  • MAFFT - Multiple sequence alignment program for linux and other unix-like operating bioinformatics systems. Offers a range of multiple alignment strategies.
  • Automated Codon Usage Analysis Software - ACUA is a freeware VB based interface for Insilico codon analysis. It provides nucleotide analysis, statistical codon analysis and positional nucleotide analysis. It presents the results in spreadsheets which can be utilized for further statistical analys
  • GDE - An integrated linux environment for bioinformatics and evolutionary biology analysis based software on the Genetic Data Environment (GDE). biology Contains binaries for Linux software and Mac OS X, biology documentation, screenshots, references, and organism specific software interfaces.
  • Seqtools - Commercial Windows software for batch handling and analysis of nucleotide biology and protein sequences.
  • Expression 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.
  • Gints - Object-oriented regulation network simulator written in Java. Includes biology downloadable software biology and documentation. The site is in biology French and English.
  • PHRED - A widely-used program for base calling DNA sequencing trace files. software Source code available and free for non-commercial users.
  • Mauve - Free software for constructing global alignments of multiple bioinformatics rearranged genomes. software The visualization environment displays sequence similarity bioinformatics profiles and annotated sequence software features.
  • Nano+Bio-Centre - Offers a range of free software tools for biology annotating an bioinformatics entire genome, assembling sequences, gap closing biology and analysis of microarrays.
  • biOpen - Commercial Mac OS X sequence analysis and structure biology visualization software.[PDF]
  • INCA - 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.
  • Bioinformatics Software Tools - Provides access to a number of tools including biological databases, software sequence allignment, analysis and manipulation tools and structural analysis tools. software Also provides a glossary of bioinformatics terms.
  • GeneRunner - A fairly old Windows sequence analysis tool for software everyday lab use. Formerly a commercial product.
  • CentiBiN: Centralities in Biological Networks - Application for the calculation and visualization of centralities for biological bioinformatics networks.
  • Sequence Analysis - A freeware Java application that does many standard software types of biology DNA and protein sequence analysis tasks.
  • WU-BLAST - The Washington University improved version of BLAST. Free software for academic software users.
  • Cytoscape - 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
  • NCBI BLAST - BLAST (Basic Local Alignment Search Tool) is a bioinformatics set of similarity search programs designed to explore bioinformatics all of the available sequence databases regardless of bioinformatics whether the query is protein or DNA.
  • MELTING - Computes, for a nucleic acid duplex, the enthalpy, software the entropy software and the melting temperature of the software helix-coil transitions.
  • Sfold - Predicts probable RNA secondary structures, assesses target accessibility, and provides biology tools for the rational design of RNA-targeting nucleic acids. The biology web server version is free for academic use.
  • BioEdit - Free Windows biological sequence alignment editor.
  • Bioinformatics Tools in Haskell - A bioinformatics library implemented in Haskell, including various bioinformatics utilities based biology on it.
  • AlmaKnowledgeServer - Text mining tool for genomics, proteomics platforms and bioinformatics drug discovery.
  • RGBG 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.
  • CodonCode Corporation - Offers CodonCode Aligner, a DNA sequence assembly, sequence alignment, contig editing and mutation detection software for Windows and Mac OS X.
  • Meta-MEME - Software toolkit for building and using motif-based hidden software Markov models biology of DNA and proteins - from software the Univ. of California-San biology Diego.
  • STRAP - Software supports the analysis of hundreds of proteins bioinformatics and integrates software aa sequence, secondary structure, 3D-structure and bioinformatics genomic- and mRNA-sequence, and software residue annotation.
  • DNAMAN - Commercial software for DNA and Protein sequence analysis software and manipulation. software Available for Windows and Mac OS software X.
  • Friend - An integrated multiple structure visualization and multiple sequence software alignment application. bioinformatics Available for Windows, Linux.
  • limmaGUI - A graphical user interface for linear modelling of software cDNA and bioinformatics oligonucleotide microarray data to identify differentially software expressed genes.
  • SeWeR - An integrated portal for common web-based bioinformatics services. Built in biology Javascript as a standalone browser application.
  • HMMER - Profiles protein sequence data using hidden Markov models bioinformatics of a statistical descriptions of a sequence family\\'s bioinformatics consensus. HMMER is a freely distributable implementation of bioinformatics profile HMM software for protein sequence analysis.
  • MIRA - A sequence assembly suite with SNP detection for "hard" projects.
  • Sockeye - 3D visualisation platform for Comparative Genomics visualisation.
  • ADF MAGE-ML - Open source Java software for checking and conversion biology of MicroArray biology Array Design data file (ADF -Array biology Design File- MAGE-ML).
  • PhyloSort - A Java tool to sort phylogenetic trees by bioinformatics searching for user-specified subtrees that contain a monophyletic bioinformatics group of interest defined by operational taxonomic units.
  • msa.cgb.ki.se - Open source software developed by Timo Lassmann for multiple sequence bioinformatics alignment, including Kalign, Kalignvu and Mumsa.
  • pDRAW32 - Freeware DNA cloning, analysis and visualization software.
  • 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.


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