Free Bioinformatics for Linux

STEPS is a package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie's SSA, extended to deal with diffusion of molecules over the elements of...

tapir is a Python tool that contains programs to estimate and plot phylogenetic informativeness for large datasets.Citing tapirWhen using tapir, please cite:- Faircloth BC, Chang J, Alfaro ME: tapir enables high throughput analysis of phylogenetic...

picme is a Python package that contains programs to estimate and plot phylogenetic informativeness for large datasets.InstallationFor the moment, the easiest way to install the program is:git clone git://github.com/faircloth-lab/picme.git /path/to/picmeTo...

tigreBrowser is a gene expression model browser for results from tigre R package (http://www.bioconductor.org/packages/release/bioc/html/tigre.html).Installation:tigreBrowser requires Python version >=2.5. tigreBrowser can be installed with the following...

checkmyclones is a software that provides tools to check Sanger sequencing results (or any plain-text or FASTQ files) against a set of reference sequences, provided in any reasonable format (including...

Syntainia is an innovative application for visualization of multiple genomes. It presents a simple and intuitive user interface to view and manipulate relationships between groups of genes. With a clearer gene visualization, it is easier for the...

CWC Simulator is a C++ implementation of CWC, a calculus for the representation and simulation of biological systems. After a successful installation (see INSTALL) you'll be able to run simulations over CWC models, as shown in some examples (see...

AREM is a based on MACS (Model Based Analysis for ChIP-Seq data).High-throughput sequencing coupled to chromatin immuno- precipitation (ChIP-Seq) is widely used in characterizing genome-wide binding patterns of transcription factors, cofactors, chromatin...

AHREA is a sofware suite that makes finding Relative Expression Learners easy. It is written in...

E-Cell System is a concept of constructing virtual cells on computers.E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells, architected by Kouichi Takahashi and...