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Tiling Microarray Analysis Tools 2 (aka T2 and TiMAT2) is a collection of software tools used for both low and high level tiling microarray data analysis using the Affymetrix, Nimblegen, and Agilent platforms. T2 is a fork of the original TiMAT project at the BDTNP. T2 is designed for processing chIP-chip, RNA difference, and comparative genomic hybridization experiments from both single and multi chip data sets. The T2 package contains 50+ command line applications built from an extensive Java code base of 250+ classes for all types of genomic analysis. T2 was build over 2.5 years at LBNL and Affymetrix by David Nix and is under continued development in our Core Bioinformatic facility.

T2 Web Site

See SourceForge T2 site for documentation and download instructions. T2 is installed on the core Linux servers, and .

Key Links:

  • Tutorial in how to use T2 to process your tiling data.
  • Results descriptions. Look here to better understand the various results generated by T2.
  • T2 Application descriptions. Look here for useful command line utilities and analysis tools.
  • Tutorial and user guide for IGB, a platform independent, integrated genome browser for visualizing all types of genomic data.


  • Want to run CorrelationMaps on chIP-chip data? See FAQ