CNA-HMMer: software for detection of DNA copy number alterations (CNAs) from array comparative genomic hybridization (aCGH) data

Author: Sohrab Shah

[NEW]: Software for "Model based clustering of array CGH data" is now posted here:
http://www.cs.ubc.ca/~sshah/acgh/hmmMix0.1.zip.
This software is an implementation of the model described in:

Sohrab P. Shah, K-John Cheung, Jr, Nathalie A. Johnson, Guillaume Alain, Randy D. Gascoyne, Douglas E. Horsman, Raymond T. Ng and Kevin P. Murphy. Model-based clustering of array CGH data Bioinformatics 2009 25(12):i30-i38

We have consolidated software used in the following publications:

S P Shah, X Xuan, R J DeLeeuw, M Khojasteh, W L Lam, R Ng, and K P Murphy. Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics, 22(14):431.439, Jul 2006. [PDF]

AND

S P Shah, W L Lam, R Ng, and K P Murphy. Modeling recurrent DNA copy number alterations in array CGH data. Bioinformatics 2007 Jul 1;23(13):i450-8 [PDF]

into a single package for multi-purpose array CGH data analysis called CNA-HMMer (pronounced CNA "hammer"). The package contains Matlab source code for detecting CNAs from a single aCGH data file and detecting recurrent CNAs across a set of aCGH data files.

Click here to download the CNA-HMMer Matlab toolbox version 0.1 (zip file)

Click here for download, installation and usage documentation for CNA-HMMer v0.1.

Should you have any questions or experience any problems, please contact Sohrab Shah at sshah@cs.ubc.ca.

NOTE: previous software called LSPHMM has now been subsumed by the CNA-HMMer Matlab toolbox. If you were using the LSPHMM code, please replace it with the CNA-HMMer toolbox.

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