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Bio-Informatics

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Showing page 1 of 118.

  • Bowtie Icon
    Bowtie

    Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.

    1,380 weekly downloads
  • Jmol Icon
    Jmol

    Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs.

    1,386 weekly downloads
  • SAM tools Icon
    SAM tools

    SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAM tools provide efficient utilities on manipulating alignments in the SAM format.

    1,275 weekly downloads
  • Burrows-Wheeler Aligner Icon
    Burrows-Wheeler Aligner

    BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

    752 weekly downloads
  • MeV Icon
    MeV

    MeV (Multiple Experiment Viewer) is a Java tool for genomic data analysis. MeV supports many different input formats, and provides an intuitive graphical interface for clustering, classification, statistical analysis and theme discovery.

    613 weekly downloads
  • picard Icon
    picard

    A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.

    498 weekly downloads
  • MrBayes Icon
    MrBayes

    MrBayes is a program for the Bayesian estimation of phylogeny.

    526 weekly downloads
  • Gwyddion Icon
    Gwyddion

    A data visualization and processing tool for scanning probe miscroscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry, useful also for general image and 2D data analysis.

    671 weekly downloads
  • Systems Biology Markup Language (SBML) Icon
    Systems Biology Markup Language (SBML)

    The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.

    487 weekly downloads
  • Primer3 - PCR primer design tool Icon
    Primer3 - PCR primer design tool

    Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.

    338 weekly downloads
  • OpenClinic GA Icon
    OpenClinic GA

    OpenClinic GA is an open source integrated hospital information management system covering management of administrative, financial, clinical, lab, x-ray, pharmacy, meals distribution and other data. Extensive statistical and reporting capabilities.

    339 weekly downloads
  • Staden Package Icon
    Staden Package

    A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

    231 weekly downloads
  • CARE2X php Integ Hospital Info System Icon
    CARE2X php Integ Hospital Info System

    Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab

    233 weekly downloads
  • The Chemistry Development Kit Icon
    The Chemistry Development Kit

    The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.

    191 weekly downloads
  • PowerTalk Icon
    PowerTalk

    PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows

    288 weekly downloads
  • SASHIMI Icon
    SASHIMI

    The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to our open mzXML format.

    201 weekly downloads
  • APBS Icon
    APBS

    APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>.

    153 weekly downloads
  • vcftools Icon
    vcftools

    A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project

    304 weekly downloads
  • FreeMED Icon
    FreeMED

    GPL-licensed Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features

    172 weekly downloads
  • VarScan Icon
    VarScan

    Variant detection in next-generation sequencing data

    171 weekly downloads
  • AMOS Icon
    AMOS

    AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.

    104 weekly downloads
  • MIRA Icon
    MIRA

    MIRA - Sequence assembler and mapper for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet. Please visit http://sourceforge.net/apps/mediawiki/mira-assembler/

    214 weekly downloads
  • BioImageXD Icon
    BioImageXD

    BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.

    91 weekly downloads
  • MUMmer Icon
    MUMmer

    MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

    125 weekly downloads
  • Generic Model Organism Database Project Icon
    Generic Model Organism Database Project

    GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.

    120 weekly downloads
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