Bio-Informatics
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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 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 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 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 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 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 MrBayes is a program for the Bayesian estimation of phylogeny.
526 weekly downloads -
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) 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 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 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 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 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 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 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 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 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 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 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 Variant detection in next-generation sequencing data
171 weekly downloads -
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 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 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 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 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
