plot" class="anchor"></a>Why did we write ‘microhaplot’?</h2>
<p>We tried to use existing tools to give us what we needed for our amplicon-based microhaplotypes.</p>
<ul>
<li>We were hopeful that <a href="http://catchenlab.life.illinois.edu/stacks/">STACKS</a> would provide us useful microhaplotypes. What we found was that the presence of indels caused STACKS to fail, and even if it didn’t we never found a reliable way to export inferred read haplotypes. (We could see what looked like haplotypes in th