Mercurial > repos > davidvanzessen > argalaxy_tools

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planemo upload commit 93519df849f317f4a8fc6167a48a4ee06e6aeff8
author rhpvorderman
date Wed, 30 Apr 2025 12:44:38 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bla/c/8/e/dataset_c8e48707-5040-4674-8189-5ebffd00b6c5_files/index.html	Wed Apr 30 12:44:38 2025 +0000
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+<div class='tabber'><div class='tabbertab' title='Gene frequencies'>
+<a href='VFPlot.pdf'><img src='VFPlot.png'/></a>
+<a href='VPlot.pdf'><img src='VPlot.png'/></a>
+<a href='JPlot.pdf'><img src='JPlot.png'/></a> <br />
+<a href='DReadingFrame.pdf'><img src='DReadingFrame.png'/></a>
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+
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+</head>
+
+<body lang=EN-US style='tab-interval:.5in'>
+
+<div class=WordSection1>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language:
+EN-GB'>Gene frequencies tab</span></u></b></p>
+
+<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
+justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>This tab gives
+information on the frequency of V, D and J gene usage. <o:p></o:p></span></p>
+
+<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
+justify;line-height:normal'><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language:
+EN-GB'>Graphs</span></b></p>
+
+<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
+justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Distribution of
+V gene families<o:p></o:p></span></u></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK121"></a><a
+name="OLE_LINK123"></a><a name="OLE_LINK122"></a><span style='mso-bookmark:
+OLE_LINK121'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";
+mso-ansi-language:EN-GB'>Bar graph showing the frequency of V gene family usage
+in all uploaded donors. </span></span><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'><o:p></o:p></span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
+justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative
+frequency of V gene usage<o:p></o:p></span></u></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><a name="OLE_LINK124"></a><a
+name="OLE_LINK126"></a><a name="OLE_LINK125"></a><span style='mso-bookmark:
+OLE_LINK124'><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";
+mso-ansi-language:EN-GB'>Bar graph showing the frequency of V genes in all
+uploaded donors. The order of the V genes on the x-axis can be altered by
+altering the “<span style='color:black;background:white'>Order of V(D)J genes
+in graphs” filter on the main page of the Immune repertoire pipeline.</span></span></span><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif";
+color:black;background:white;mso-ansi-language:EN-GB'><o:p></o:p></span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
+justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative
+frequency of D gene usage<o:p></o:p></span></u></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language:
+EN-GB'>Bar graph showing the frequency of D genes in all uploaded donors. The
+order of the D genes on the x-axis can be altered by altering the “<span
+style='color:black;background:white'>Order of V(D)J genes in graphs” filter on
+the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
+justify;line-height:normal'><u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif";mso-ansi-language:EN-GB'>Relative
+frequency of J gene usage<o:p></o:p></span></u></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language:
+EN-GB'>Bar graph showing the frequency of J genes in all uploaded donors. The
+order of the J genes on the x-axis can be altered by altering the “<span
+style='color:black;background:white'>Order of V(D)J genes in graphs” filter on
+the main page of the Immune repertoire pipeline.<o:p></o:p></span></span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><o:p>&nbsp;</o:p></p>
+
+<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt;text-align:
+justify;line-height:normal'><u><span style='font-size:12.0pt;font-family:"Times New Roman","serif"'>D
+reading frame<o:p></o:p></span></u></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif";mso-ansi-language:
+EN-GB'>Bar graph visualizing the frequency by which each D reading frame is
+used in each donor.</span></p>
+
+</div>
+
+</body>
+
+</html>
+</div>
+<div class='tabbertab' title='CDR3 Characteristics'>
+<a href='CDR3LengthPlot.pdf'><img src='CDR3LengthPlot.png'/></a><br />
+<a href='AAComposition.pdf'><img src='AAComposition.png'/></a>
+<table class='pure-table pure-table-striped'>
+<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>
+</table>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
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+<body lang=EN-US>
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+<div class=WordSection1>
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+<p class=MsoNormalCxSpFirst style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><b><u><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>CDR3 characteristics tab</span></u></b></p>
+
+<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>This tab gives information on the
+different characteristics of the CDR3.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><b><span lang=EN-GB style='font-size:
+12.0pt;font-family:"Times New Roman","serif"'>Graphs</span></b></p>
+
+<p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>length distribution of CDR3</span></u></p>
+
+<p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>Graph visualizing for each donor the
+distribution of the CDR3 length in amino acids between all sequences.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>Amino acid composition of CDR3</span></u></p>
+
+<p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>Bar graph visualizing for each donor how
+frequent each amino acid is used in the CDR3 of all sequences. The red colour
+in the background indicate positively charged amino acids, and the blue colour
+in the background indicate negatively charged amino acids. The amino acids are
+ordered from hydrophilic (left) to hydrophobic (right). </span></p>
+
+<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><b><span lang=EN-GB style='font-size:
+12.0pt;font-family:"Times New Roman","serif"'>Table</span></b></p>
+
+<p class=MsoNoSpacing style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>Table showing for each donor the median
+CDR3 length.</span></p>
+
+<p class=MsoNormal><span lang=EN-GB>&nbsp;</span></p>
+
+</div>
+
+</body>
+
+</html>
+</div>
+<div class='tabbertab' title='Heatmaps'><div class='tabber'>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
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+
+<p class=MsoNormalCxSpFirst style='text-align:justify'><span style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>In this tab
+heatmaps are provided showing the frequency of different combinations V and D,
+D and J and V and J genes according together. For each donor a subtab with all
+three heatmaps is provided.</span></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>
+</div></div>
+<div class='tabbertab' title='Compare Heatmaps'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>
+</table><div name='comparisonarea'>
+<table><tr id='comparison_table_vd'></tr></table>
+<table><tr id='comparison_table_vj'></tr></table>
+<table><tr id='comparison_table_dj'></tr></table>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+<!--
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+
+<p class=MsoNormalCxSpFirst style='text-align:justify'><span style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The tab allows
+you to compare the VD, VJ and DJ heatmaps of multiple donors to each other. </span></p>
+
+<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family:
+"Times New Roman","serif"'>By ticking the include box of a donor, the three
+heatmaps of this donor is visualized underneath eachother. By clicking the
+include box of multiple replicates the heatmaps of these replicates are visualized
+next to each other allowing easy comparison of heatmaps. </span></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>
+</div></div>
+<div class='tabbertab' title='Circos'><div class='tabber'>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
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+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family:
+"Times New Roman","serif"'>Martin Krzywinski, Jacqueline Schein, &#304;nanç
+Birol, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones and Marco
+A. Marra (2009). Circos: An information aesthetic for comparative genomics. In <i>Genome
+Research 10.1101/gr.092759.109</i>.</span></p>
+
+<p class=MsoNormal><span style='font-size:12.0pt;line-height:115%;font-family:
+"Times New Roman","serif"'>Circos plot showing the V-D, V-J, and D-J gen usage.
+The thicker the line the more frequent this gene combination is used.</span></p>
+
+</div>
+
+</body>
+
+</html>
+</div></div>
+<div class='tabbertab' title='Downloads'>
+<table class='pure-table pure-table-striped'>
+<thead><tr><th>Description</th><th>Link</th></tr></thead>
+<tr><td>All outputs below in a zip file</td><td><a href='all_outputs.zip'>Download</a></td></tr>
+<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>
+<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>
+<tr><td>The dataset used to generate the distribution of V gene families graph</td><td><a href='VFFrequency.txt'>Download</a></td></tr>
+<tr><td>The dataset used to generate the relative frequency of V gene usage graph</td><td><a href='VFrequency.txt'>Download</a></td></tr>
+<tr><td>The dataset used to generate the relative frequency of J gene usage graph</td><td><a href='JFrequency.txt'>Download</a></td></tr>
+<tr><td>The dataset used to generate the relative frequency of the D reading frame graph</td><td><a href='DReadingFrame.txt'>Download</a></td></tr>
+<tr><td colspan='2' style='background-color:#E0E0E0;'>CDR3 Characteristics</td></tr>
+<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.txt'>Download</a></td></tr>
+<tr><td>The dataset used to generate the Amino Acid Composition in the CDR3 graph</td><td><a href='AAComposition.txt'>Download</a></td></tr>
+<tr><td colspan='2' style='background-color:#E0E0E0;'>Heatmaps</td></tr>
+<tr><td colspan='2' style='background-color:#E0E0E0;'>Circos</td></tr>
+<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>
+<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, none)</td><td><a href='clonalityComplete.txt'>Download</a></td></tr>
+</table>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=UTF-8">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+<!--
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+</style>
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+</head>
+
+<body lang=EN-US>
+
+<div class=WordSection1>
+
+<p class=MsoNormalCxSpFirst style='text-align:justify'><b><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
+tab</span></u></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Description</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+filtered dataset:</span></u><span style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> <a name="OLE_LINK15"></a><a
+name="OLE_LINK14">Allows you to download information on V D and J gene usage,
+the junctions and the amino acid sequence of the sequences that passed the chosen
+filter settings. Note: this file contains only 1 sequences of a replicate
+sequence. </a></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Gene
+frequencies</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>The dataset used to generate the distribution
+of V gene families graph:</span></u><span style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'> Downloads a table with information used to generate
+the distribution of V gene families graph.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>The dataset used to generate  the
+distribution of D gene families graph: </span></u><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>Downloads a table with information used
+to generate the distribution of D gene families graph.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to generate the relative frequency of V gene usage graph:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data used to generate the relative frequency of V gene usage
+graph. In addition information on the chromosomal order of the V genes can be
+found.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to generate the relative frequency of D gene usage graph:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data used to generate the relative frequency of D gene usage
+graph. In addition information on the chromosomal order of the D genes can be
+found.<u> </u></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to generate the relative frequency of J gene usage graph: </span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Downloads
+the data used to generate the relative frequency of J gene usage graph. In
+addition information on the chromosomal order of the J genes can be found.<u> </u></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
+color:black'>The dataset used to generate the relative frequency of the D
+reading frame graph</span></u><span lang=EN-GB style='font-size:12.0pt;
+line-height:115%;font-family:"Times New Roman","serif";color:black'>: Downloads
+the data used to generate the relative frequency of the D reading frame. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
+color:black'>CDR3 characteristics</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='margin-bottom:0in;margin-bottom:.0001pt;
+text-align:justify;line-height:normal'><u><span style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>The dataset used to generate the CDR3
+length frequency graph:</span></u><span style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'> Downloads a table with information used for the
+length distribution of CDR3 plot. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to generate the Amino Acid Composition in the CDR3 graph:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the frequency of the different amino acids in the CDR3 of all
+filtered sequences. This data set is used for the generation of the Amino Acid
+Composition in the CDR3 graph. In addition the order of amino acids based on hydrophobicity
+in included. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Heatmaps</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the VD heatmap for “donor name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the VD heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the VJ heatmap for “donor name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the VJ heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the DJ heatmap for “sample name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the DJ heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Circos</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the VD circus plots for “donor name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the VD heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the VJ circus plots for “donor name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the VJ heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the DJ circus plots for “sample name”:</span></u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Downloads the data set used for the generation of the DJ heatmap. For each
+uploaded donor a separate download is generated.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Clonality</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+dataset used to calculate clonality score: </span></u><span style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Allows you to
+download information on V D and J gene usage, the junctions and the amino acid
+sequence of the sequences that passed the chosen filter settings. Note: this
+file contains all the replicate sequences form the different input files.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Sequences
+that are present in more than one replicate:</span></u><span style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'> Allows you to
+download a table containing all the sequences that were present in more than
+one replicate. It provides the concidence type, clonaltype, sequence name,
+replicate number, and the nucleotide sequence</span></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+</div>
+
+</body>
+
+</html>
+</div></html>