SimHap v1.0.0 release notes

Since the Beta 2.1 release, SimHap has been given a face lift. With an updated 'look and feel' and a plethora of new functionality, SimHap v1.0.0 is a comprehensive statistical analysis tool for genetic epidemiology. 

New features include:
* An updated graphical user interface with a new logo
* A stand alone R package for users who want the flexibility of a command-line interface
* Histogram generation of quantitative traits with and without log transformations, including a Shapiro-Wilks normality test
* Natural log and log base-10 transformation options for quantitative response variables
* The option of independent haplotype frequency generation in cases and controls
* Finer selection options for setting the haplotype frequency threshold
* Ability to cancel haplotype analysis jobs part way through 
* Analysis of matched case-control data for epidemiological, SNP and haplotype models
* Prediction of genotypic and haplotypic marginal means for quantitative traits
* Allele frequency counts automatically calculated and displayed at the onset of SNP analysis, and major allele set as the one with the highest frequency
* Warnings when the expected number of individuals with a particular haplotype is less than 10
* More comprehensive summary statistics with the facility to print results from screen 
* More comprehensive error messages including a warning if non-biallelic SNPs exist in the genotype file (useful for data checking)
* Corrections and enhancements to previously identified bugs (including fix to likelihood ratio test when genotype data is missing)

Note: SimHap v1.0.0 requires Java 1.5+, R 2.4.0+ and the SimHap R package installed. Please see user manual for details on where to obtain these.