Top Most Downloaded Bio-Informatics Software

A Free (GPL) Science & education program for WindowsJmol is a great, free (gpl) program only available for Windows, being part of the category Science & education software with subcategory Astronomy and has been created by JMol Team.More about JmolThis program is available for users with the operating system Wi...

Simulate electrophysical models for medical researchI'm forever trying to replicate single-cell electrophysical models in my bedroom but I normally end up just eating doughnuts and playing on the Playstation instead. I think my luck has changed though thanks to CESE. The program simulates the surroundings of electrophy...

Perform searches using the combined power of multiple enginesQube - abbreviated as q3, is a revolutionary concept in browsing and searching the internet. The developers call it a "Next generation, websearch client for instant, single-click access to information from the collective index of traditional search engines".T...

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....

A data visualization and processing tool for scanning probe microscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry data, useful also for general image and 2D data analysis. Support for more than 130 SPM file formats.All standard functions: levelling, geometrical transforms, statistical characterisation,...

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. Support Illumina, SOLiD, 454, Sanger reads, PacBio reads and assembly contigsGapped alignment and paired-end mappingAccurate,...

PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and a...

The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detecti...

SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samt...

This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DN...

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/>. Please register at http://eepurl.com/by4eQr before downloa...

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....

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. Focused on limited resource hospitalsMultilingual: english, french, du...

Please use WebMeV for all NGS and Microarray analysis: http://mev.tm4.org/...

A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/ Parse VCF filesOutput Population Genetic Statistics ...

QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. QUAST computes a number of well-known metrics, including contig accuracy, number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and in the manual). A comprehensive ana...

Java Treeview - An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format...

A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogen...

Combenefit software is a standalone application for Windows that performs surface analyses of drug and other agent combinations to identify synergy. Please cite as: "Di Veroli,G.Y. et al. (2016) Combenefit: an interactive platform for the analysis and visualization of drug combinations. Bioinformatics." (http://bioinf...

CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files....