s<a class="anchor" aria-label="anchor" href="#arg-sample-sets"></a></dt>
<dd><p>A list (optionally a named list) of character vectors with
individual names (one vector per set)</p></dd>


<dt id="arg-mode">mode<a class="anchor" aria-label="anchor" href="#arg-mode"></a></dt>
<dd><p>The mode for the calculation ("sites" or "branch")</p></dd>


<dt id="arg-windows">windows<a class="anchor" aria-label="anchor" href="#arg-windows"></a></dt>
<dd><p>Coordinates of breakpoints between windows. The first
coordinate 