SimHap
When inferring haplotypes for individuals with ambiguous phase (e.g. phase unknown genotype data), uncertainty is inherent. SimHap uses biallelic SNP genotype data to impute haplotype frequencies at the individual level.

JLIN
JLIN (Java LINkage disequilibrium plotter) is designed for customisable, intuitive visualisation of LD analysis across all common computing platforms. Customisation allows the researcher to choose particular visualisation, statistical measures and measurement ranges.

Celestial3D
A graphical presentation of familial data (e.g. phenotypic, genotypic or demographic) and pedigree structures can show important information in a far less cluttered fashion, enabling rapid analysis and interpretation of results.

JLGraph
JLGraph provides a simple, automated solution to creating graphical displays of all 22 human chromosomes on a single page. JLGraph allows the user to input one or two data files along with axis labels, dataset labels and an output title for the page produced.