on matrix can be provided for the simulation of the correlatedBdEffects.</li>
<li>Short option flags for command-line use of <em>PhenotypeSimulator</em> were removed.</li>
</ol>
<p><strong>Output</strong></p>
<ol>
<li>
<em>PhenotypeSimulator</em> provides the option to save the simulated phenotypes and genotypes in formats compatible with a number of commonly used genetic association software (gemma, bimbam, plink, snptest) via writeStandardOutput.</li>
<li>Intermediate phenotype components are now saved pe