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<!DOCTYPE HTML>
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	<title> AGCoL </title>
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<table style="width: 800px; border: 2px solid #999999; padding: 0; border-spacing:0; margin-left: auto; margin-right: auto;">
<tr><td colspan="3" style="height: 105px; background-color: rgb(204, 204, 204);">
<img src="img/banner5.png" name="banner" alt="AGCOL BANNER" height="105" width="815">
<tr><td style="vertical-align: text-top;">

<table>
<tr><td style="height: 4px"><td>
<tr><td style="vertical-align: text-top;"><!--- left side --->
 	<table>
	<tr><td>&nbsp;
		<td style="background-color: #eaeaea" class="c"> &nbsp; <b> Home of the Soderlund lab </b>
	<tr><td style="height: 4px"><td>
	<tr><td>&nbsp;
		<td class="c"> <i>&nbsp;The Soderlund lab is part of the
			<a href="http://www.bio5.org" target="_blank" title="External link to BIO5 Home Page">
				BIO5 Institute </a> at the University of Arizona </i> <br>
	<tr><td>&nbsp;
		<td class="c"> <img alt="" src="img/bullet_blue.gif" class=a>
			<a href="./lab/lab.html"> Lab </a> | <a href="./lab/pubs.html"> Publications </a> | <a href="https://github.com/csoderlund"> Github </a>

	<tr><td style="height: 15px"><td>
	<tr><td style="height: 15px width=8px"> &nbsp;
		<td style="background-color: #eaeaea" class="c"> &nbsp; <b> Actively Supported Software </b>
	<tr><td style="height: 4px"><td>
	<tr><td> &nbsp;
		<td class="c"> <img alt="" src="img/bullet_blue.gif" class="a">
			<ttp>SyMAP Synteny mapping and analysis program</ttp> <br>
				Compute the synteny between two sequences genomes. Query and view two or more genomes at a time. <br>
				<a href="https://csoderlund.github.io/SyMAP/">Download and documentation</a>
	<tr><td style="height: 8px"><td>
	<tr><td> &nbsp;
		<td class="c"> <img alt="" src="img/bullet_blue.gif" class="a">
			<ttp>TCW Transcriptome computational workbench</ttp> <br>
				Build and query an annotated database with gene ontology and differential expression. Build and query a comparative transcriptome database. <br>
				<a href="https://csoderlund.github.io/TCW/">Download and documentation</a>

	<tr><td style="height: 15px"><td>
	<tr><td style="height: 15px width=8px"> &nbsp;
		<td style="background-color: #eaeaea" class="c"> &nbsp; <b>Other Software</b>
	<tr><td style="height: 8px"><td>
	<tr><td> &nbsp;
		<td class="c"> <img alt="" src="img/bullet_blue.gif" class="a">
			<ttp>AW Allele Workbench for allele-specific expression</ttp> <br>
			A pipeline to compute heterozygous SNPs from RNAseq data. Compute Allele Imbalance (AI). Query and view the results. <br>
		 <a href="https://csoderlund.github.io/AW/">Download and documentation</a>
	<tr><td style="height: 8px"><td>
	<tr><td style="height: 15px width=8px"> &nbsp;
	<td class="c"> <img alt="" src="img/bullet_blue.gif" class="a">
			<ttp>FPC FingerPrinted Contigs for building physical maps</ttp> <br>
				Compute a physical map from restriction fragments. Query and view the resulting contigs.
				See <a href="lab/FPC.html">FPC</a>.
	<tr><td style="height: 15px"><td>
	<tr><td style="height: 15px width=8px"> &nbsp;
		<td style="background-color: #eaeaea" class="c"> &nbsp;<b>Supported by</b>
	<tr><td style="height: 55px width=8px"> &nbsp;
		<td style="height: 55">
			<table style="width: 434">
			<tr><td style="text-align: center; width: 8%">
					<a href="http://www.bio5.org"><img src="img/bio5.gif"
					alt="BIO5" style="border: 0px solid ; width: 36px;"></a><br>
						<font size="1">BIO5</font>
				<td style="text-align: center; width: 10%">
					<a href="http://www.arizona.edu">
						<img alt="University of Arizona" src="img/UA.gif"
						style="border: 0px solid ; width: 36px;"></a><br>
						<font size="1">UA</font>
				<td style="text-align: center; width: 12%">
						<a href="http://nsf.gov/">
						<img src="img/NSF.gif" alt="National Science Foundation"
						style="border: 0px solid ; width: 36px;"></a><br>
						<font size="1">NSF</font>

				<td style="text-align: center; width: 10%">
						<a href="http://www.usda.gov/"><img src="img/USDA.gif"
						alt="United States Department of Agriculture"
						style="border: 0px solid ; width: 32px;"></a><br>
						<font size="1">USDA</font>
				</table>
	</table>

	<td> <!--- right side --->
		<table>
		<tr><td><small><b>SyMAP</b>: Circle</small>
				<br><a href="img/symap-circle.png">
				<img src="img/symap-circle.png" alt="Circle" style="border: 1px solid black; width: 115px;"> </a>
			<td style="vertical-align: text-top;"><small>3 species chromosomes</small>
				<br><a href="img/symap.png">
				<img src="img/symap.png" alt="Dotplot" style="border: 1px solid black; width: 135px;"> </a>

		<tr><td colspan=2><small>Dot Plot</small>
				<br><a href="img/symap-dot.png">
				<img src="img/symap-dot.png" alt="2D" style="border: 1px solid black; width: 170px;"> </a>


		<tr><td colspan=2><small><b>TCW</b>: Transcriptome analysis</small>
				<br><a href="img/tcw.png">
				<img src="img/tcw.png" alt="viewSingleTCW" style="border: 1px solid black; width: 250px;"> </a>
		<tr><td colspan=2><small>Alignment of 3 species transcripts</small>
				<br><a href="img/tcw-cmp.png">
				<img src="img/tcw-cmp.png" alt="viewMultiTCW" style="border: 1px solid black; width: 200px;"> </a>

		<tr><td colspan=2><small><i>Click any image for close up</i></small>
		</table>
 </table>
</table>
<table style="width: 800; margin: 0 auto;">
	<tr><td style="text-align: center;" class="c"> Email: <a href="mailto:cas1@arizona.edu"> cas1@arizona.edu </a>
</table>
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