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Bioinformatics Advance Access originally published online on December 20, 2005
Bioinformatics 2006 22(4):512-513; doi:10.1093/bioinformatics/btk012
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

FLOSS: flexible ordered subset analysis for linkage mapping of complex traits

B. L. Browning

Genetic Data Sciences, GlaxoSmithKline Five Moore Drive, P.O. Box 13398, Research Triangle Park NC 27709, USA

Summary: The FLOSS software package is a flexible framework for ordered subset analysis. FLOSS is specifically designed for use with the Merlin linkage analysis package, but FLOSS can be used with any linkage analysis software package that reports NPL Z-scores for each locus and family. When FLOSS is used with the Merlin linkage analysis package, one can use either non-parametric Z-scores or Kong and Cox linear allele sharing model LOD scores. Monte Carlo P-values are calculated using a permutation test with an efficient Besag–Clifford sequential stopping rule. FLOSS also has a flexible tool for assigning family covariate scores from Merlin input files. FLOSS includes user documentation and is written in Java for easy portability. The FLOSS source code is documented and designed to be extensible.

Availability: http://www.stat.auckland.ac.nz/~browning/floss/floss.htm

Contact: brian_browning1{at}yahoo.com

Received on December 14, 2005; accepted on December 15, 2005

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