alignment program</strong>. <code>microhaplot</code> does not do alignments. You have to provide aligned data to it. From the aligned data, <code>microhaplot</code> can extract the bases sequenced at the desired locations.</li>
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<code>microhaplot</code> <strong>is not a haplotype phasing program</strong>. There is no special algorithm going on in <code>microhaplot</code> to try to assemble haplotypes (across reads or loci, for example.) It merely uses the simple fact that a single sequencing read will c