Copy Number
Variation Expectation Maximisation
program which graphically and numerically presents CNV allele and
genotype distributions. Complex CNVs (eg the salivary amylase locus)
are typically assayed as a total copy number (aggregating both allelic
copy numbers). CoNVEM can be used to determine the most likely
population allele and genotype frequencies from these copy number
counts, enabling inferences to be made about mutational history and
population allellic architecture. Hum Mutat. 2010
Jan 14.


CubeX provides the exact solutions
to
Hill's cubic equation for haplotype frequency between two loci. Whilst
this is often satisfactorily solved using an expectation maximisation
approach, under certain circumstances more than one biologically
possible solution to the equation may exist. Given the nine diplotype
counts for a pair of biallelic markers, CubeX will present all
biologically possible solutions. BMC
Bioinformatics 2007, 8:428


An HWE calculator with analysis
for
ascertainment bias. This program is particularly relevant to Mendelian
Randomisation analyses, where it is important to evaluate missingness
under different genetic models. Analagous to the "intention to treat"
analysis in RCTs, MR analyses should include "intention to analyse".
The calculator is also of general utility as a quick test of
HardyWeinberg equilibrium. Am J Epidemiol.
2009 February 15; 169(4): 505514.


MIDAS implements an
expectationmaximisation approach to the analysis of interallelic
linkage disequilibrium analysis between any pairwise combination of
multiallelic and biallelic markers. An interactive graphical interface
enables the user to visualise the linkage disequilibrium across many
markers. BMC
Bioinformatics 2006, 7:227


Calculates odds ratio for each combination of genotypes enabling (graphical) evaluation of genetic model. The results are presented graphically as OR
with 95% confidence intervals and in tabular format. This tool compares the heterozygote odds ratios (Het vs Hom11 and Hom22 vs Het) to the homozygote odds
ratio (Hom22 vs Hom11) to facilitate interpretation of genetic model (additive, multiplicative, dominant, recessive etc.)

