Software Bioinformatics Biology

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

• Top/Business/Healthcare/Computing/Software

• STRING - Search for Tandem Repeats IN Genomes. Includes C source code and examples.
  
• KoriBlast - Commercial graphical software for Blast searches.
  
• Sockeye - 3D visualisation platform for Comparative Genomics visualisation.
  
• MELTING - Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.
  
• GoCore - GoCore is a free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
  
• MaGe (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.
  
• limmaGUI - A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
  
• ADF MAGE-ML - Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
  
• MedScan - Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
  
• PhyloSort - 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.
  
• DNPTrapper - A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
  
• Nano+Bio-Centre - Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.
  
• 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.
  
• Genespotter - Commercial Windows software for analyzing biochip image data.
  
• AlmaKnowledgeServer - Text mining tool for genomics, proteomics platforms and drug discovery.
  
• Tandem Repeats Finder - Locates and displays tandem repeats in DNA sequences.
  
• Genome-tools Web Interface - Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.
  
• DNA Baser - Sequence assembly software package including a free tool for merging multiple FASTA files into a single FASTA file.
  
• MIRA - A sequence assembly suite with SNP detection for "hard" projects.
  
• Bioinformatics Tools in Haskell - A bioinformatics library implemented in Haskell, including various utilities based on it.
  
• GDE - 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.
  
• 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
  
• SeWeR - An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
  
• Meta-MEME - Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
  
• PHRED - A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commercial users.
  
• XDigitize - A Linux/Unix visualization software system for evaluation of hybridisation experiments.
  
• DNAMAN - Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
  
• Phrap/Consed - DNA sequence assembler and finishing tools from the UW Genome Center.
  
• Premier 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.
  
• Unipro UGENE: Integrated Bioinformatics Tools - Free cross-platform bioinformatics software package for DNA and protein sequence analysis.
  
• NEXML: Phylogenetic Data in xml - Exchange standard for representing phylogenetic data, inspired by the commonly used NEXUS format but more robust and easier to process.
  
• gsuffix - 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.
  
• 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.
  
• BioMAJ - Workflow engine dedicated to bio-data synchronization and processing.
  
• Bioinformatics 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.
  
• MAFFT - Multiple sequence alignment program for linux and other unix-like operating systems. Offers a range of multiple alignment strategies.
  
• FASTA - William Pearson's package for fast sequence comparison tools.
  
• STRAP - Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation.
  
• APBioKnoppix - Knoppix based bioinformatics software tools. Bootable from CD.
  
• Darwin - An interactive tool for peptide and nucleotide sequence analysis.
  
• Biomax 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.
  
• Sequence Analysis - A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
  
• Sfold - 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.
  
• GeneSifter - Provides complete systems for data-intensive genetic analysis applications like microarrays and next gen sequencing-based transcription. From Geospiza, Seattle, USA.
  
• Geneious - 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.
  
• CentiBiN: Centralities in Biological Networks - Application for the calculation and visualization of centralities for biological networks.
  
• 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.
  
• msa.cgb.ki.se - Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa.
  
• Gints - Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
  
• Seqtools - Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
  
• Biological Concept Diagram Editor - A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes.
  
• ARCiB -- 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 structural biology, for software packages on various platforms.
  
• Friend - An integrated multiple structure visualization and multiple sequence alignment application. Available for Windows, Linux.
  
• pDRAW32 - Freeware DNA cloning, analysis and visualization software.
  
• JAligner - Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
  
• biOpen - Commercial Mac OS X sequence analysis and structure visualization software. [PDF]
  
• The 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
  
• Biochemfusion: Enabling Biochemformatics - Software for working with post-translationally or chemically modified peptides and proteins including proteins as both sequences and chemical structures.
  
• 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
  
• WU-BLAST - The Washington University improved version of BLAST. Free for academic users.
  
• HMMER - 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.
  
• CodonCode Corporation - Offers CodonCode Aligner, a DNA sequence assembly, sequence alignment, contig editing and mutation detection software for Windows and Mac OS X.
  
• JSTRING - Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format.
  
• GeneRunner - A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product.
  
• Mauve - Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features.
  
• NCBI 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.
  
• MARBL - MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.
  
• BioEdit - Free Windows biological sequence alignment editor.
  
• sys-bio.org - Software for simulating metabolic, signal and genetic networks. Home of SBW, Jarnac, JDesigner and winSCAMP.
  
• 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.
  
  

Copyright © 1995-2009 Internet Advertising Solutions, Inc.
Copyright Notice | Privacy Policy | Site Map | APR