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robjgiff committed May 28, 2024
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<meta charset="UTF-8">
<title>Flavivirid-GLUE by giffordlabcvr</title>
<title>Flavivirus-GLUE by giffordlabcvr</title>
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" type="text/css" href="../assets/stylesheets/normalize.css" media="screen">
<link href='https://fonts.googleapis.com/css?family=Open+Sans:400,700' rel='stylesheet' type='text/css'>
Expand All @@ -22,8 +22,8 @@ <h2 class="project-tagline">Resources for comparative genomic analysis of flaviv
<a href="../../index.html" class="btn">Home</a>
<a href="./viruses.html" class="btn">Viruses</a>
<a href="./news.html" class="btn">News</a>
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/zipball/master" class="btn">Download</a>
<a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE/tree/master" class="btn">GitHub</a>
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/zipball/master" class="btn">Download</a>
<a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/tree/master" class="btn">GitHub</a>
</section>

<section class="main-content">
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<b>Please note</b>: links to files on GitHub are mainly designed to indicate where
these files are located within the repository.
To investigate files (e.g. tree files) in the appropriate software context we recommend
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/zipball/master"><b>downloading the entire repository</b></a>
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/zipball/master"><b>downloading the entire repository</b></a>
and browsing locally.

</p>
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<li>
The complete list of <b>vertebrate</b> genomes screened can be found
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/blob/master/digs/vertebrate-genomes-screened.csv"><b>here</b></a>.
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/blob/master/digs/vertebrate-genomes-screened.csv"><b>here</b></a>.
</li>


<li>
The complete list of <b>invertebrate</b> genomes screened can be found
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/blob/master/digs/invertebrate-genomes-screened.csv"><b>here</b></a>.
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/blob/master/digs/invertebrate-genomes-screened.csv"><b>here</b></a>.
</li>

<li>
The set of <b>flavivirus</b> polypeptide sequences used as probes can be found
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/blob/master/digs/flavi-probes.faa"><b>here</b></a>.
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/blob/master/digs/flavi-probes.faa"><b>here</b></a>.
</li>

<li>
The final set of <b>flavivirus</b> and <b>EFV</b> polypeptide sequences used as
references can be found
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/blob/master/digs/flavi-references.faa"><b>here</b></a>.
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/blob/master/digs/flavi-references.faa"><b>here</b></a>.
</li>

<li>
Input parameters for screening using the
<a target="_blank" href="https://giffordlabcvr.github.io/DIGS-tool/"><b>DIGS tool</b></a>
can be found
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/blob/master/digs/efv-screen-digs.ctl"><b>here</b></a>.
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/blob/master/digs/efv-screen-digs.ctl"><b>here</b></a>.
</li>
</ul>

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<a target="_blank" href="http://glue-tools.cvr.gla.ac.uk/#/coreSchema"><b>core schema</b></a>
to allow the capture of EFV-specific data.
These schema extensions are defined in
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/blob/master/glue/build/eve/efvSchemaExtensions.glue"><b>this file</b></a>
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/blob/master/glue/build/eve/efvSchemaExtensions.glue"><b>this file</b></a>
and comprise two additional table: 'locus_data' and 'refcon_data'.
Both tables are linked to the main 'sequence' table via the 'sequenceID' field.
</p>
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<p>
Raw FASTA for EFVs recovered via
<a target="_blank" href="https://giffordlabcvr.github.io/DIGS-tool/">database-integrated genome screening (DIGS)</a>
are <a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/tree/master/sources/fasta-digs-eve"><strong>here</strong></a>.
are <a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/tree/master/sources/fasta-digs-eve"><strong>here</strong></a>.
</p>



<p>
Sequence-associated data in tabular format are <a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/blob/master/tabular/eve/efv-side-data.tsv"><strong>here</strong></a>.
Sequence-associated data in tabular format are <a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/blob/master/tabular/eve/efv-side-data.tsv"><strong>here</strong></a>.
The tabular files contain information about the genomic locations of EFVs.
</p>

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<p>
EFV consensus/reference FASTA is
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/tree/master/sources/fasta-refseqs-eve"><strong>here</strong></a>.
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/tree/master/sources/fasta-refseqs-eve"><strong>here</strong></a>.
</p>



<p>
Tabular formatted metadata for EFV reference sequences is
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/blob/master/tabular/eve/efv-refseq-side-data.tsv"><strong>here</strong></a>.
<a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/blob/master/tabular/eve/efv-refseq-side-data.tsv"><strong>here</strong></a>.
</p>


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Trees were constructed at distinct taxonomic levels:

<ol>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE/tree/master/trees/major-lineage"><strong>Major lineage-level</strong></a> phylogenies</li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE/tree/master/trees/minor-lineage"><strong>Minor lineage-level</strong></a> phylogenies</li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE/tree/master/trees/genus"><strong>Genus-level</strong></a> phylogenies</li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE/tree/master/trees/subgenus"><strong>Subgenus-level</strong></a> phylogenies</li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/tree/master/trees/major-lineage"><strong>Major lineage-level</strong></a> phylogenies</li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/tree/master/trees/minor-lineage"><strong>Minor lineage-level</strong></a> phylogenies</li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/tree/master/trees/genus"><strong>Genus-level</strong></a> phylogenies</li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/tree/master/trees/subgenus"><strong>Subgenus-level</strong></a> phylogenies</li>
</ol>

</p>
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<footer class="site-footer">
<span class="site-footer-owner"><a href="https://github.com/giffordlabcvr/Flavivirus-GLUE/">Flavivirid-GLUE</a> is maintained by <a href="https://github.com/giffordlabcvr">giffordlabcvr</a>.</span>
<span class="site-footer-owner"><a href="https://github.com/giffordlabcvr/Flavivirus-GLUE-EVE/">Flavivirid-GLUE</a> is maintained by <a href="https://github.com/giffordlabcvr">giffordlabcvr</a>.</span>
<span class="site-footer-credits">This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the <a href="https://github.com/jasonlong/cayman-theme">Cayman theme</a> by <a href="https://twitter.com/jasonlong">Jason Long</a>.</span>
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