feat(about): Updated the about page to contain more up-to-date inform…

…ation.
Ecogenomics · Mar 11, 2022 · ad3f878 · ad3f878
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       <v-card-text class="text--primary">
 
-        The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial
-        taxonomy based on genome phylogeny, primarly funded by an <a
-        href="https://www.uq.edu.au/news/article/2015/06/uq-leads-nation-prestigious-arc-laureate-fellowships"
-        target="_blank">Australian
-        Research Council Laureate Fellowship</a>. <br>
-        <br>
-        The genomes used to construct the phylogeny are obtained from
-        <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">RefSeq</a> and
-        <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">Genbank</a>, and GTDB releases are indexed
-        to
-        RefSeq releases, starting with release 76.
-        Importantly and increasingly, this dataset includes draft genomes of uncultured
-        microorganisms
-        obtained from metagenomes and single cells, ensuring improved genomic representation of the
-        microbial world.
-        All genomes are independently quality controlled using <a
-        href="https://github.com/Ecogenomics/CheckM/wiki" target="_blank">CheckM</a> before inclusion in GTDB,
-        see
-        statistics
-        <NuxtLink :to="latestStatsPageUrl">here</NuxtLink>
-        . <br>
-        <br>
-        The GTDB taxonomy is based on genome trees inferred with <a
-        href="http://www.microbesonline.org/fasttree/" target="_blank">FastTree</a> from an aligned concatenated
-        set of 120 single copy marker proteins for Bacteria, and with IQ-TREE from a concatenated
-        set of 122 marker proteins for Archaea
-        (download
-        page
-        <NuxtLink to="/downloads">here</NuxtLink>
-        ).
-        Additional marker sets are also used to cross-validate tree topologies including
-        concatenated
-        ribosomal proteins and ribosomal RNA genes.<br>
-        <br>
-        <a href="https://www.ncbi.nlm.nih.gov/taxonomy" target="_blank">NCBI taxonomy</a> was initially used to
-        decorate
-        the genome tree via <a href="http://tax2tree.sourceforge.net/" target="_blank">tax2tree</a>.
-        The 16S rRNA-based <a href="http://greengenes.secondgenome.com" target="_blank">Greengenes</a> and
-        <a href="https://www.arb-silva.de/" target="_blank">SILVA</a> taxonomies are used
-        to supplement the taxonomy particularly in regions of the tree with no cultured
-        representatives.
-        <a href="https://lpsn.dsmz.de/" target="_blank">LPSN</a> is used as the primary taxonomic authority for
-        establishing naming priorities.
-        Taxonomic ranks are normalised using <a
-        href="https://github.com/dparks1134/PhyloRank" target="_blank">phylorank</a> and the taxonomy manually
-        curated to remove polyphyletic groups.
-        Polyphyly and rank evenness can be visualised in phylorank
-        <NuxtLink :to="latestStatsPageUrl">plots</NuxtLink>
-        .<br>
-        <br>
-        The GTDB taxonomy can be queried and downloaded through a number of tools on this website.
+        <p>
+          The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy
+          based on genome phylogeny, primarily funded by the <a href="https://www.arc.gov.au/" target="_blank">Australian Research Council</a> via a
+          <a href="https://www.uq.edu.au/news/article/2015/06/uq-leads-nation-prestigious-arc-laureate-fellowships" target="_blank">Laureate Fellowship</a>
+          (<a href="https://app.dimensions.ai/details/grant/grant.5129370" target="_blank">FL150100038</a>) and Discovery Project
+          (<a href="https://dataportal.arc.gov.au/NCGP/Web/Grant/Grant/DP220100900" target="_blank">DP220100900</a>),
+          with the welcome assistance of <a href="https://research.uq.edu.au/research-support/research-management/funding-schemes/uq-internal-schemes" target="_blank">strategic funding from
+          The University of Queensland.</a>
+        </p>
+
+        <p>
+          The genomes used to construct the phylogeny are obtained from <a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">RefSeq</a>
+          and <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">GenBank</a>, and GTDB
+          releases are indexed to RefSeq releases, starting with release 76. Importantly and increasingly,
+          this dataset includes draft genomes of uncultured microorganisms obtained from metagenomes and single
+          cells, ensuring improved genomic representation of the microbial world. All genomes are independently
+          quality controlled using <a href="https://github.com/Ecogenomics/CheckM/wiki" target="_blank">CheckM</a> before inclusion in GTDB,
+          see statistics <NuxtLink :to="latestStatsPageUrl">here</NuxtLink>.
+        </p>
+
+        <p>
+          The GTDB taxonomy is based on genome trees inferred with <a
+          href="http://www.microbesonline.org/fasttree/" target="_blank">FastTree</a> from an aligned concatenated set of
+          120 single copy marker proteins for Bacteria, and with <a href="http://www.iqtree.org/">IQ-TREE</a> from a concatenated set of 53
+          (starting with R07-RS207) and 122 (prior to R07-RS207) marker proteins for Archaea (download page <NuxtLink to="/downloads">here</NuxtLink>).
+          Additional marker sets are also used to cross-validate tree topologies including concatenated ribosomal
+          proteins and ribosomal RNA genes. <a href="https://www.ncbi.nlm.nih.gov/taxonomy" target="_blank">NCBI taxonomy</a> was initially used to decorate the genome tree via
+          <a href="http://tax2tree.sourceforge.net/" target="_blank">tax2tree</a> and subsequently used as a reference source of new taxonomic opinions including new names.
+          The 16S rRNA-based <a href="http://greengenes.secondgenome.com" target="_blank">Greengenes</a> and <a href="https://www.arb-silva.de/" target="_blank">SILVA</a> taxonomies were intially used to supplement the taxonomy
+          particularly in regions of the tree with no cultured representatives, however genome assembly
+          identifiers are now used to create placeholder names for uncultured taxa. <a href="https://lpsn.dsmz.de/" target="_blank">LPSN</a> is used as the
+          primary nomenclatural reference for establishing naming priorities and nomenclature types. All t
+          axonomic ranks except species are normalised using <a href="https://github.com/dparks1134/PhyloRank" target="_blank">PhyloRank</a> and the taxonomy manually curated to
+          remove polyphyletic groups. Polyphyly and rank evenness can be visualised in PhyloRank <NuxtLink :to="latestStatsPageUrl">plots</NuxtLink>.
+          Delineation of species was initially done based on phylogeny and rank normalization but was
+          substituted with the ANI-based method (starting with R04-RS89) to enable scalable and automated assignment of genomes to species clusters.
+        </p>
+
+        <p>
+          The GTDB taxonomy can be queried and downloaded through a number of tools on this website. Classification of new genomes based on GTDB framework can be done via
+          <a href="https://github.com/Ecogenomics/GTDBTk" target="_blank">GTDB-Tk</a>.
+        </p>
+
 
         <!-- The team -->
         <div class="d-block mt-10 ">