CELLULOID: tumour cellularity and ploidy tool.

A pragmatic tool to evaluate ploidy, cellularity, clonal and sub-clonal populations from tumour whole genome sequencing data, and to appropriately derive absolute copy numbers profiles.

The following programs are gzip'ed tar archives, and are designed to run under a UNIX/Linux operating system. They are provided “as is” and are not being supported anymore.

SUP: an extension to SLINK to allow a larger number of marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with a trait locus. This version of SUP is meant to be used only with version 3.0 or above of FastSLINK (released in March 2010). Using version 3.0 of FastSLINK, there's no upper limit to the number of founders a pedigree may have. Also, by using “slink -t” instead of “slink”, the trait locus genotypes are now readily available in a new output file, which simplifies the whole simulation set up. For the older version of SUP, click here.

GENEHUNTER++sad: implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing.

SimM: a gene dropping simulation software.

nucular: a program that splits extended pedigrees into nuclear families, with the option of recoding all sibs as half-sibs with distinct mothers of fathers.

The description of SimM can be found here:


The description of nucular can be found here:


The articles related to the above programs can be found following these links:

Schäffer AA, Lemire M, Ott J, Lathrop GM, Weeks DE (2011) Coordinated Conditional Simulation with SLINK and SUP of Many Markers Linked or Associated to a Trait in Large Pedigrees. Hum Hered 71:126-134.

Lemire M (2006) SUP: An extension to SLINK to allow a larger number of marker loci to be simulated bin pedigrees conditional on trait values. BMC Genetics 2006, 7:40 (about SUP)

Lemire M, Roslin NM, Laprise C, Hudson TJ, Morgan K (2004) Transmission-ratio distortion and allele sharing in affected sib pairs: a new linkage statistic with reduced bias, with application to chromosome 6q25.3. Am J Hum Genet 75:571–586 (about GENEHUNTER++sad and SimM)

Lemire M (2005) A simple nonparametric multipoint procedure to test for linkage through mothers or fathers as well as imprinting effects in the presence of linkage. BMC Genetics 2005, 6(Suppl 1):S159 (about nucular)

[Mathieu Lemire's Contact Information]