Bio-Informatics
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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.
1,983 weekly downloads -
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.
1,385 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.
1,063 weekly downloads -
Open Babel Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, biochemistry, or related areas
723 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.
597 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.
529 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
444 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.
408 weekly downloads -
picard A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.
416 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.
420 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.
319 weekly downloads -
MrBayes MrBayes is a program for the Bayesian estimation of phylogeny.
799 weekly downloads -
OpenVista (R) OpenVista(R) is the open-source version of VistA, an enterprise grade health care information system developed by the U.S. Veterans Affairs and deployed at 1,500 global facilities. OpenVista is a registered trademark of Medsphere Systems Corporation
277 weekly downloads -
Java Treeview Java Treeview - An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format
361 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.
256 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.
187 weekly downloads -
JGAP JGAP is a Genetic Algorithms and Genetic Programming package written in Java. It is designed to require minimum effort to use, but is also designed to be highly modular. JGAP features grid functionality and a lot of examples. Many unit tests included.
226 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://apbs.sf.net/>.
187 weekly downloads -
MIRA MIRA - Sequence assembler for whole genome shotgun and EST sequencing data. Can use Sanger, 454, Solexa (Illumina) and IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet. Please visit http://sourceforge.net/apps/mediawiki/mira-assembler/
159 weekly downloads -
The igraph library This is another library for creating and manipulating graphs. There is simply no other graph library out there which can handle graphs of the size the author is confronted with. Whenever possible igraph tries to be also user friendly and portable.
183 weekly downloads -
SourceAFIS Fingerprint recognition library for .NET and experimentally for Java
147 weekly downloads -
PerlPrimer PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.
171 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
239 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
234 weekly downloads -
BisKit Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs.
166 weekly downloads
