 input, in that order.</p>

    </div>

    <h3>Input</h3>
    <div class="indent">
      <p>Sequences in <a href="fasta-format.html">FASTA format</a> from the <code>&lt;FASTA file&gt;</code>.</p>
      <p>An index generated from the sequences with  <a href="fasta-make-index.html">fasta-make-index</a>
      which is named the same as the FASTA file but with ".index" appended.</p>
      <p>Sequence identifiers, either listed on the command line,
      from a file specified with <span class="popt">-f</span> o