Golden Helix, SNP and variation Suite is mainly targeted for SNP, CNV , GWAS analysis. The latest version provides NGS analysis tools. Its modular design enables the facilitation of usability upgrades.

This software has a unique approach that enables the direct comparison of GWAS and sequencing results.

TM4 is a software suite for the analysis of microarrays, developed at the Dana-Farber Cancer Institute, 44 Binney St, Boston, MA, USA.

The TM4 suite of tools consist of four major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment Viewer (MeV), as well as a Minimal Information About a Microarray Experiment (MIAME)-compliant MySQL database, all of which are freely available to the scientific research community at TIGR's Software Download Site. Although these software tools were developed for spotted two-color arrays, many of the components can be easily adapted to work with single-color formats such as filter arrays and GeneChips™(Affymetrix). Three of the TM4 applications, MADAM, MIDAS, and MeV, were developed in Java; TIGR Spotfinder was written in C/C++. The TM4 software system represents a comprehensive, extensible, open-source, and freely available collection of tools that we believe will be of use to a wide range of laboratories conducting microarray experiments. We further hope that by providing source code along with the executable software, we can encourage others to new analysis methods and utilities that will further enhance the capabilities of this software system.

TM4 is free, open-source software released under the Artistic license. This license is OSI certified.

Partek^® Genomics Suite^TM is a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data. The software is unique in supporting all microarray and next generation sequencing technologies including gene expression and digital gene expression (DGE), exon/alternative splicing and RNA-Seq, copy number and association, ChIP-chip, ChIP-seq, and microRNA in a single software package, allowing for analysis of multiple applications in one complete solution.

OnechannelGui is an addon software to affylmGui written by Raffale A Calogero, Bioinformatics and Genomics Unit, Dept. of Clinical and Biological Sciences Torino (Italy). This package is an add-on of affylmGUI enabling Quality Control, statistical analysis and data mining (GO analysis, clustering) for one channel microarray data. It supports EXON  arrays and Illumina bead arrays.