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Updated EVE links
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@robjgiff
robjgiff committed May 27, 2024
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Expand Up @@ -23,8 +23,8 @@ <h2 class="project-tagline">Resources for comparative genomic analysis of parvov
<a href="./viruses.html" class="btn">Viruses</a>
<a href="./highlights.html" class="btn">Highlights</a>
<a href="./tutorial.html" class="btn">Tutorial</a>
<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/zipball/master" class="btn">Download</a>
<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/tree/master" class="btn">GitHub</a>
<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/zipball/master" class="btn">Download</a>
<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/tree/master" class="btn">GitHub</a>
</section>

<section class="main-content">
Expand Down Expand Up @@ -87,7 +87,7 @@ <h3>
<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/Parvovirus-GLUE/zipball/master"><b>downloading the entire repository</b></a>
<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/zipball/master"><b>downloading the entire repository</b></a>
and browsing locally.

</p>
Expand Down Expand Up @@ -119,32 +119,32 @@ <h3>

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

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

<li>
The final set of <b>parvovirus</b> and <b>EPV</b> polypeptide sequences used as
references can be found

<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/digs/digs-reference-library/digs-reference-library-aa.fasta"><b>here</b></a>.
<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/digs/digs-reference-library/digs-reference-library-aa.fasta"><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/Parvovirus-GLUE/blob/master/digs/epv-screen-digs.ctl"><b>here</b></a>.
<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/digs/epv-screen-digs.ctl"><b>here</b></a>.
</li>

</ul>
Expand Down Expand Up @@ -205,23 +205,23 @@ <h3>
<p>
Raw data in tabular format are can be found at the following links/directories:
<ol>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/parvovirinae/epv-amdo-refseqs-side-data.tsv">Amdoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/parvovirinae/epv-erythro-refseqs-side-data.tsv">Erythyroparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/parvovirinae/epv-dependo-refseqs-side-data.tsv">Dependoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/parvovirinae/epv-proto-refseqs-side-data.tsv">Protoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/hamaparvovirinae/epv-ichthama-refseqs-side-data.tsv">Ichthamaparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/parvovirinae/epv-amdo-refseqs-side-data.tsv">Amdoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/parvovirinae/epv-erythro-refseqs-side-data.tsv">Erythyroparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/parvovirinae/epv-dependo-refseqs-side-data.tsv">Dependoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/parvovirinae/epv-proto-refseqs-side-data.tsv">Protoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/hamaparvovirinae/epv-ichthama-refseqs-side-data.tsv">Ichthamaparvoviruses</a></li>
</ol>

</p>

<p>
Nucleotide level data in FASTA format (individual files), can be found at the following links/directories:
<ol>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/tree/master/sources/genus/amdo/fasta-refseqs-amdo-epv">Amdoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/sources/genus/erythro/fasta-refseqs-erythro-epv">Erythyroparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/sources/genus/dependo/fasta-refseqs-dependo-epv">Dependoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/sources/genus/proto/fasta-refseqs-proto-epv">Protoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/sources/genus/ichthama/fasta-refseqs-ichthama-epv">Ichthamaparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/tree/master/sources/genus/amdo/fasta-refseqs-amdo-epv">Amdoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/sources/genus/erythro/fasta-refseqs-erythro-epv">Erythyroparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/sources/genus/dependo/fasta-refseqs-dependo-epv">Dependoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/sources/genus/proto/fasta-refseqs-proto-epv">Protoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/sources/genus/ichthama/fasta-refseqs-ichthama-epv">Ichthamaparvoviruses</a></li>
</ol>
</p>

Expand All @@ -242,14 +242,14 @@ <h3>
data structure. Alignments in the project include:

<ol>
<li> A single ‘<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/alignments/root/parvo-ns-root+eves.aln"><strong>root</strong></a>’
<li> A single ‘<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/alignments/root/parvo-ns-root+eves.aln"><strong>root</strong></a>’
alignment constructed to represent proposed
homologies between representative members of major parvovirus lineages
(including extinct lineages represented only by EPVs).</li>
<li> ‘<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/tree/master/alignments/internal/genus/"><strong>Genus-level</strong></a>’
<li> ‘<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/tree/master/alignments/internal/genus/"><strong>Genus-level</strong></a>’
alignments constructed to represent proposed homologies between the genomes of
representative members of specific parvovirus genera and EPV reference sequences.
<li> ‘<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/tree/master/alignments/tips/"><strong>Tip</strong></a>’
<li> ‘<a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/tree/master/alignments/tips/"><strong>Tip</strong></a>’
alignments in which all taxa are derived from a single EPV lineage.</li>
</ol>

Expand Down Expand Up @@ -277,9 +277,9 @@ <h3>
Trees were constructed at distinct taxonomic levels:

<ol>
<li> Recursively populated <a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/tree/master/trees/family-root"><strong>root</strong></a> phylogeny (Rep)</li>
<li> <a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/tree/master/trees/genus-level-with-eves/"><strong>Genus-level</strong></a> phylogenies</li>
<li> <a href="https://github.com/giffordlabcvr/Parvovirus-GLUE/tree/master/trees/eve-orthologs/"><strong>EPV lineage-level</strong></a> phylogenies</li>
<li> Recursively populated <a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/tree/master/trees/family-root"><strong>root</strong></a> phylogeny (Rep)</li>
<li> <a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/tree/master/trees/genus-level-with-eves/"><strong>Genus-level</strong></a> phylogenies</li>
<li> <a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/tree/master/trees/eve-orthologs/"><strong>EPV lineage-level</strong></a> phylogenies</li>
</ol>

</p>
Expand Down Expand Up @@ -313,23 +313,23 @@ <h3>
<p>
Raw data in tabular format are can be found at the following links:
<ol>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/parvovirinae/epv-amdo-side-data.tsv">Amdoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/parvovirinae/epv-erythro-side-data.tsv">Erythyroparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/parvovirinae/epv-dependo-side-data.tsv">Dependoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/parvovirinae/epv-proto-side-data.tsv">Protoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/tabular/eve/hamaparvovirinae/epv-ichthama-side-data.tsv">Ichthamaparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/parvovirinae/epv-amdo-side-data.tsv">Amdoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/parvovirinae/epv-erythro-side-data.tsv">Erythyroparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/parvovirinae/epv-dependo-side-data.tsv">Dependoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/parvovirinae/epv-proto-side-data.tsv">Protoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/tabular/eve/hamaparvovirinae/epv-ichthama-side-data.tsv">Ichthamaparvoviruses</a></li>
</ol>

</p>

<p>
Nucleotide level data in FASTA format (individual files), can be found at the following links:
<ol>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/tree/master/sources/genus/amdo/fasta-digs-amdo-epv">Amdoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/sources/genus/erythro/fasta-digs-erythro-epv">Erythyroparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/sources/genus/dependo/fasta-digs-dependo-epv">Dependoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/sources/genus/proto/fasta-digs-proto-epv">Protoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/sources/genus/ichthama/fasta-digs-ichthama-epv">Ichthamaparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/tree/master/sources/genus/amdo/fasta-digs-amdo-epv">Amdoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/sources/genus/erythro/fasta-digs-erythro-epv">Erythyroparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/sources/genus/dependo/fasta-digs-dependo-epv">Dependoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/sources/genus/proto/fasta-digs-proto-epv">Protoparvoviruses</a></li>
<li> <a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/sources/genus/ichthama/fasta-digs-ichthama-epv">Ichthamaparvoviruses</a></li>
</ol>
</p>

Expand All @@ -347,7 +347,7 @@ <h3>
<a target="_blank" href="http://glue-tools.cvr.gla.ac.uk/#/coreSchema"><b>core schema</b></a>
to allow the capture of EVE-specific data.
These schema extensions are defined in
<a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE/blob/master/glue/build/core/parvoSchemaExtensions.glue"><b>this file</b></a>
<a target="_blank" href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/blob/master/glue/build/core/parvoSchemaExtensions.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>
Expand Down Expand Up @@ -488,7 +488,7 @@ <h3>


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<span class="site-footer-owner"><a href="https://github.com/giffordlabcvr/Parvovirus-GLUE-EVE/">Parvovirus-GLUE</a> is maintained by <a href="https://github.com/giffordlabcvr">giffordlabcvr</a>.</span>

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