Windows

Allinea MAP

Allinea MAPis a profiler for serial and parallel applications written in C, C++, FORTRAN 77, Fortran 90. It supports multiple parallel programming paradigms including MPI, and OpenMP.

Affymetrix Tiling Analysis

The TAS software provides analysis capabilities specifically for Affymetrix GeneChip Tiling Arrays. 

Xcalibur

Thermo Scientific Xcalibur software is a flexible Windows*-based data system that provides instrument control and data analysis for the entire family of Thermo Scientific mass spectrometers and related instruments.

Windows QTL Cartographer

Windows QTL Cartographer is a tool for mapping quantitative traits. It allows importing and exporting data in various formats and also includes a powerful tool for summarizing and presenting results.

SOAPdenovo

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

FreeSurfer

FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

Qiime

QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. 

IPA - Ingenuity Pathway Analysis

Ingenuity Pathways Analysis (IPA) is a software and database search tool for finding functions and pathways for specific biological states. It is a web-delivered application that makes use of the Ingenuity Pathways Knowledge Base, a currated database consisting of millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. It currently has data for humans, rats, and mice.

Haploview -- Haplotype analysis

Haploview is a graphical program for haplotype analysis. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals.

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