Citius

With the support of the Walloon Region of Belgium, Direction Generale de l'Agriculture

   

Citius is a program to apply Markov Chain Monte Carlo (MCMC) method to calculate multilocus genotype probabilities and to analyse genes shared identical by descent (IBD).

Citius uses pedigree data, molecular records for codominant marker loci and quantitative trait data.

• Calculates ordered genotype probabilities for individuals with no records using MCMC algorithm.
• Calculates approximate probabilities for ordered genotypes using iterative peeling.
• Calculates IBD sharing statistics for all pairs of relatives.
• Calculates IBD gametic matrix.
• Perform disease mapping by analysing genes shared IBD among affecteds.

Citius helps solving several genetic problems. Output from Citius can be used in:

• model free desease mapping
• homozygosity mapping
• QTL mapping via variance component method
• tests based on identity by descent
• marker assisted selection (MAS) and genotype assisted selection (GAP)

Citius is fast software utilizing several advanced techiques. It supports research on large data sets in human and animal genetics.

• Developed for very large complex pedigrees. Succesfull applications involve thousands individuals.
• Advanced sampler generates genotype configurations for entire pedigree jointly ensuring extremely good mixing behaviour.
• Multiple computational shortcuts including genotype elimination and allele set-recoding ensure high performance.

Citius is available freely for academic scientific research. If you have a question please send email.

Downloads:

• manual
• executable file for Linux (AMD Opteron)
• useful PERL script

Examples:

• MCMC estimation of multilocus genotype probabilities from incomplete marker data. pedigree data control file
• Estimation of genotype probabilities from incomplete marker data by the use of iterative peeling. pedigree data control file
• Monte Carlo estimation of mixed model that includes major gene effect and polygenic effect. Computation according to Guo and Thompson (1994, Biometrics 50: 417-432). The algorithm uses jointly EM and Gibbs sampler. pedigree data control file
• Unitrait BLUP-AM. pedigree data control file
• Two-trait BLUP-AM. pedigree data control file