h covalent modifications alphabet</a>
    </ol>

    <h3>Format Specification</h3>
    <div class="indent">
      <p>The alphabet definition contains the following sections:</p>
      <ol>
        <li><a href="#spec_header">Header</a></li>
        <li><a href="#spec_core">Core Symbols</a></li>
        <li><a href="#spec_ambig">Ambiguous Symbols and Aliases</a></li>
      </ol>

      <h4 id="spec_header">Header</h4>
      <div class="indent">
        <p>The header line signals that the file is an alphabet d