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opt_uparseout.html
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opt_uparseout.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html lang="en">
<head>
<meta content="en-us" http-equiv="Content-Language"/>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type"/>
<meta content="no-cache, no-store, must-revalidate" http-equiv="Cache-Control"/>
<meta content="no-cache" http-equiv="Pragma"/>
<meta content="0" http-equiv="Expires"/>
<title>
allpairs_global command
</title>
<link href="stylesx.css" rel="stylesheet" type="text/css"/>
<style type="text/css">
body.c4 {background-color:#c0c0c0;}
div.c3 {position:absolute; top:45px; left:20px; width:830px; background-color:#ffffff; border-width:10px; border-style:solid;border-color:white;}
span.c2 {font-weight: bold}
div.c1 {position:absolute; top:10px; left:20px; width:850px; height:60px;}
.TopButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
.TopButton { color:white; }
a.TopButton:link { text-decoration:none; }
a.TopButton:visited { text-decoration:none; }
a.TopButton:hover { color:orange; }
.NewButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
.NewButton { color:white; }
a.NewButton:link { text-decoration:none; }
a.NewButton:visited { text-decoration:none; }
a.NewButton:hover { color:orange; }
.SideButtonPara { color:white; font-family:Arial, Helvetica, sans-serif; font-size:9pt; font-weight:normal; text-align:center; line-height:18px; }
.SideButton { color:white; }
a.SideButton:link { text-decoration:none; }
a.SideButton:visited { text-decoration:none; }
a.SideButton:hover { color:orange; }
</style>
</head>
<body style="background-color:#c0c0c0;">
<div>
<a href="https://drive5.com/usearch">
<img alt="USEARCH v12" src="usearch12_banner.jpg" style="position:absolute; top:40px; left:10px; padding:0px; border:0px;"/>
</a>
</div>
<div style="position:absolute; top:115px; left:10px; width:850px; background-color:#ffffff; min-height:500px">
<div style="position:relative; float:left; background-color:#696969; width:125px; left: 0px; min-height:500px; padding:5px; height: 125px;">
<div class="SideButtonPara" style="text-align:center; padding-top:5px;">
<a class="SideButton" href="index.html">
Docs home
</a>
<br/>
<hr style="border:0; border-bottom: 1px solid white;"/>
<a class="SideButton" href="cmds.html">
Commands
</a>
<br/>
<a class="SideButton" href="topics.html">
Topics
</a>
<br/>
<a class="SideButton" href="citation.html">
Publications
</a>
<br/>
</div>
</div>
<div class="ManText" style="left:20px; position: absolute; left:135px; width:695px; background-color:white; padding:10px">
<h1>
-uparseout option
</h1>
<p>
<span class="ManText">
Output file, UPARSE tabbed format. Supported by
<a href="cmd_cluster_otus.html">
cluster_otus
</a>
and
<a href="cmd_uparse_ref.html">
uparse_ref
</a>
. There are five or six fields, as shown in the following table.
</span>
</p>
<div align="left">
<table border="0" cellpadding="3" cellspacing="0" summary="Table" width="577">
<tr>
<td align="right" class="c2" valign="top">
<span class="ManText">
Field
</span>
</td>
<td class="c3" valign="top" width="5">
</td>
<td class="c3" valign="top" width="512">
<span class="ManText c4">
Description
</span>
</td>
</tr>
<tr>
<td align="right" class="c5" valign="top">
<span class="ManText">
1
</span>
</td>
<td class="c5" width="5">
</td>
<td class="c5" width="512">
<span class="ManText">
Query
<a href="sequence_labels.html">
label
</a>
.
<br/>
</span>
</td>
</tr>
<tr>
<td align="right" class="c3" valign="top">
<span class="ManText">
2
</span>
</td>
<td class="c3" width="5">
</td>
<td class="c3" width="512">
<span class="ManText">
<a href="mock_classes.html">
Classification
</a>
.
</span>
<p>
<span class="ManText">
For cluster_otus, this field is otu, match or chimera.
<br/>
<b>
otu
</b>
: New OTU. Sequence is <97% to existing OTU and is not chimeric.
<br/>
<b>
match
</b>
: Assigned to existing OTU (>= 97% match).
<br/>
<b>
chimera
</b>
: Sequence is chimeric.
</span>
</p>
<p>
<span class="ManText">
For uparse_ref, it is perfect, good, noisy, chimera or other.
<br/>
<b>
perfect
</b>
: 100% match to a reference sequence.
<br/>
<b>
good
</b>
: >=99% match to reference sequence.
<br/>
<b>
noisy
</b>
: >= 97% match to reference sequence
<br/>
<b>
chimera
</b>
: matches chimeric model constructed from reference sequences
<br/>
<b>
other
</b>
: < 97% match and not chimeric.
<br/>
</span>
</p>
</td>
</tr>
<tr>
<td align="right" class="c5" valign="top">
<span class="ManText">
3
</span>
</td>
<td class="c5" width="5">
</td>
<td class="c5" width="512">
<span class="ManText">
Percent
<a href="identity.html">
identity
</a>
between the query sequence and the top hit in the reference database. With cluster_otus, the reference database is the current set of OTUs. If no hit was found, this field is set to *,
<br/>
</span>
</td>
</tr>
<tr>
<td align="right" class="c3" valign="top">
<span class="ManText">
4
</span>
</td>
<td class="c3" width="5">
</td>
<td class="c3" width="512">
<span class="ManText">
Percent identity between the query sequence and the
<a href="uparseref_algo.html">
maximum parsimony model
</a>
. If no model is made, e.g. because the database is empty, then this field is set to *.
<br/>
</span>
</td>
</tr>
<tr>
<td align="right" class="c5" valign="top">
<span class="ManText">
5
</span>
</td>
<td class="c5" width="5">
</td>
<td class="c5" width="512">
<span class="ManText">
OTU label(s). If the model is chimeric, then the labels and start-end segment coordinates are given. Otherwise, the label of the reference sequence. For cluster_otus, this will be the label of an existing OTU. If no model is constructed, this field is set to *.
<br/>
</span>
</td>
</tr>
</table>
</div>
<p>
<span class="ManText c4">
Example output
</span>
</p>
<p class="ManCode">
<span class="ManCode">
Even1.7;size=4383; otu * * OTU_1
<br/>
Even1.145;size=21; otu * * OTU_2
<br/>
Even1.1733;size=20; match 99.5 * OTU_2
<br/>
Even1.942;size=20; chimera 94.0 100.0 OTU_1(1-141)+OTU_2(142-200)
<br/>
Even1.1821;size=20; match 98.5 * OTU_1
<br/>
Even1.1415;size=19; match 97.0 * OTU_2
<br/>
</span>
</p>
</div>
</div>
</body>
</html>