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<h1>COIL: Complexity Of Infection Likelihood calculator</h1>
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<p>
Complex malaria infections are defined as those containing more than one genetically
distinct lineage of Plasmodium parasite. Complexity of infection (COI) is a useful
parameter to estimate from patient blood samples because it is associated with clinical
outcome, epidemiology, and disease transmission rate. COIL is a method for estimating
COI using likehood from a panel of genotyping assays for bi-alellic SNPs. Please see
the <a href="user.shtml">User Guide</a> for a complete set of instructions.
</p>

<p>To run COIL, select an input file using the <b>Browse</b> button below, then click
<b>Submit</b>.</p>

<form action="cgi-bin/coil.cgi" method="post" enctype="multipart/form-data">
  <table>
    <tr>
      <td>Barcodes file</td>
      <td><input type="file" name="barcodes" /></td>
    </tr>

    <tr>
      <td>MAFs file (optional)</td>

      <td><input type="file" name="mafs" /></td>
    </tr>
  </table><input type="submit" value="Submit" />
</form>

<p>Data from submitted input files are not kept on Broad servers.</p>

<h2>Citation</h2>

<p>
Galinsky K, Valim C, Salmier A, de Thoisy B, Musset L, Legrand E, Faust A,
Baniecki ML, Ndiaye D, Daniels RF, Hartl DL, Sabeti PC, Wirth DF, Volkman SK,
Neafsey DE. COIL: a methodology for evaluating malarial complexity of infection
using likelihood from single nucleotide polymorphism data. Malar J. 2015 Jan
19;14(1):4. <a href="http://www.ncbi.nlm.nih.gov/pubmed/25599890">PubMed PMID: 25599890</a>; PubMed Central PMCID:
PMC4417311.
</p>

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