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Top: Science: Biology: Bioinformatics: Software:

Software

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Editor's Picks:

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

Sites:

» ADF MAGE-ML Open in a new browser window - Open source Java software for checking and conversion of MicroArray Array Design data file (ADF -Array Design File- MAGE-ML).
» APBioKnoppix Open in a new browser window - Knoppix based bioinformatics software tools. Bootable from CD.
» ARCiB -- Accessible Retired Computers in Biology Open in a new browser window - 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.
» AlmaKnowledgeServer Open in a new browser window - Text mining tool for genomics, proteomics platforms and drug discovery.
» AnnHyb Open in a new browser window - 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.
» BioEdit Open in a new browser window - Free Windows biological sequence alignment editor.
» Biological Concept Diagram Editor Open in a new browser window - A tool designed for efficient knowledge and data capture from electronic resources for sharing, mining and presentation purposes.
» DNA Counter Open in a new browser window - Small free Windows program to calculate nucleotides frequencies in DNA sequences.
» DNAMAN Open in a new browser window - Commercial software for DNA and Protein sequence analysis and manipulation. Available for Windows and Mac OS X.
» DNPTrapper Open in a new browser window - An Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
» Darwin Open in a new browser window - An interactive tool for peptide and nucleotide sequence analysis.
» Expression Profiler Open in a new browser window - 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.
» FASTA Open in a new browser window - William Pearson's package for fast sequence comparison tools.
» FASTA Convertor Open in a new browser window - Free Windows tool for merging multiple FASTA files into a single FASTA file.
» Friend Open in a new browser window - An integrated multiple structure visualization and multiple sequence alignment application. Avaliable for Windows, Linux
» GDE Open in a new browser window - 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.
» GeneRunner Open in a new browser window - A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
» Genespotter Open in a new browser window - Commercial Windows software for analyzing biochip image data.
» Genome-tools Web Interface Open in a new browser window - Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.
» Gints Open in a new browser window - Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
» GoCore Open in a new browser window - GoCore is an free Excel based tool for protein sequence alignment, comparisons and functional predictions in a simple, visually appealing, manner.
» HMMER Open in a new browser window - 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.
» INCA - INteractive Codon Analysis Open in a new browser window - 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 Open in a new browser window - Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
» JSTRING Open in a new browser window - Java program for searching Tandem Repeats (TR) in a DNA sequence. It shows the results also in a graphical format.
» Keck Computational Systems Biology Software Open in a new browser window - Software for simulating metabolic, signal and genetic networks. Home of Jarnac, JDesigner and SCAMP.
» MAFFT Open in a new browser window - Multiple sequence alignment program for linux and other unix-like operating systems. Offers a range of multiple alignment strategies.
» MARBL Open in a new browser window - MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.
» MELTING Open in a new browser window - Computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.
» MIRA Open in a new browser window - A sequence assembly suite with SNP detection for "hard" projects.
» MaGe (Magnifying Genomes) - Microbial genome Annotation System Open in a new browser window - The MaGe system offers a set of graphical interfaces which allow biologist to perform relevant expert annotation of microbial genomes.
» Mauve Open in a new browser window - Free software for constructing global alignments of multiple rearranged genomes. The visualization environment displays sequence similarity profiles and annotated sequence features.
» MedScan Open in a new browser window - Commercial Windows natural language processing software for the automated extraction of biological data from scientific literature.
» Meta-MEME Open in a new browser window - Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
» NCBI BLAST Open in a new browser window - 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.
» Nano+Bio-Centre Open in a new browser window - Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.
» PHRED Open in a new browser window - A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users.
» Phrap/Consed Open in a new browser window - DNA sequence assembler and finishing tools from the UW Genome Center.
» Premier Biosoft International Open in a new browser window - 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 Open in a new browser window - 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 & XP.
» STRAP Open in a new browser window - Software supports the analysis of hundreds of proteins and integrates aa sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence, and residue annotation.
» STRING Open in a new browser window - Search for Tandem Repeats IN Genomes. Includes C source code and examples.
» SeWeR Open in a new browser window - An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
» Seqtools Open in a new browser window - Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
» Sequence Analysis Open in a new browser window - A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
» Sfold Open in a new browser window - 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.
» Sockeye Open in a new browser window - 3D visualisation platform for Comparative Genomics visualisation.
» Tandem Repeats Finder Open in a new browser window - Locates and displays tandem repeats in DNA sequences.
» The ARB Project Open in a new browser window - 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
» WU-BLAST Open in a new browser window - The Washington University improved version of BLAST. Free for academic users.
» XDigitize Open in a new browser window - A Linux/Unix visualization software system for evaluation of hybridisation experiments.
» biOpen Open in a new browser window - Commercial Mac OS X sequence analysis and structure visualization software.
» limmaGUI Open in a new browser window - A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.
» msa.cgb.ki.se Open in a new browser window - Open source software developed by Timo Lassmann for multiple sequence alignment, including Kalign, Kalignvu and Mumsa.
» pDRAW32 Open in a new browser window - Freeware DNA cloning, analysis and visualization software.


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Category Editor: illdiletantte

Last Updated: 2007-04-03 05:33:11


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