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TamaraNaboulsi merged 1 commit into from
Feb 3, 2026
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Update "Species trees" page for e116 #936

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12 changes: 6 additions & 6 deletions ensembl/htdocs/info/genome/compara/species_trees.html
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Expand Up @@ -15,18 +15,18 @@ <h1 id="speciestrees">Species trees</h1>
The Compara pipelines use two main species trees.
</p>
<ol>
<li>The <a href="https://www.ncbi.nlm.nih.gov/taxonomy">NCBI taxonomy</a> (i.e. topology only) is typically used for non-vertebrate divisions in:
<li>The <a href="https://www.ncbi.nlm.nih.gov/taxonomy">NCBI taxonomy</a> (i.e. topology only) may be used for:
<ul>
<li>the <a href="/info/genome/compara/homology_method.html">Protein-trees</a> pipeline</li>
<li>the CAFE (Gene Gain/Loss tree) pipelines</li>
<li>the <a href="/info/genome/compara/homology_method.html">Protein-trees</a> pipelines</li>
<li>the <a href="/info/genome/compara/ncRNA_methods.html">ncRNA-trees</a> pipelines, with three sub-trees &mdash; Eutheria, Sauria, and Clupeocephala &mdash; flattened in the default Vertebrates ncRNA-trees</li>
<li>CAFE (Gene Gain/Loss tree) analyses</li>
</ul>
</li>
<li>A tree with branch-lengths computed in-house (available for download <a href="https://github.com/Ensembl/ensembl-compara/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/conf/vertebrates/species_tree.branch_len.nw">here</a>) is used for Vertebrates pipelines, including:
<li>A tree with branch-lengths computed in-house (available for download <a href="https://github.com/Ensembl/ensembl-compara/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/conf/vertebrates/species_tree.branch_len.nw">here</a>) may be used for:
<ul>
<li>the <a href="/info/genome/compara/homology_method.html">Protein-trees</a> and <a href="/info/genome/compara/ncRNA_methods.html">ncRNA-trees</a> pipelines</li>
<li>the <a href="/info/genome/compara/multiple_genome_alignments.html">Multiple-alignment</a> pipelines <sup>&dagger;</sup></li>
<li>the <a href="/info/genome/compara/conservation_and_constrained.html">Constrained Elements / Conservation Scores</a> pipelines</li>
<li>the CAFE (Gene Gain/Loss tree) pipelines</li>
<li>CAFE (Gene Gain/Loss tree) analyses</li>
</ul>

Briefly, the tree is computed as follows:
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