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@twalsh-ebi changes redone
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Via misuse of git push --force, accidentally overwrote the changes
suggested by @twalsh-ebi and approved by @ens-sb and myself.
I replicated the suggestion and [hopefully] fixed the issue.
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EreboPSilva committed Feb 11, 2025
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18 changes: 16 additions & 2 deletions ensembl/htdocs/Mus_musculus_strains.inc
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<h2>Comparative analysis</h2>

<p>We generated a multiple genome alignment of all the genomes from the The Mouse Genomes Project with <i>Mus musculus</i>, <i>Rattus norvegicus</i> and additional four Mus species using our EPO pipeline. Additionally, we have computed a LastZ alignment of <i>Mus musculus</i> and <i>Mus spretus</i>.</p>
<p>Using our EPO pipeline, we generated a multiple genome alignment of 16 of the
reference-quality genomes from the The Mouse Genomes Project with <i>Mus
musculus</i>, <i>Rattus norvegicus</i> and an additional three <i>Mus</i>
species&colon; <i>Mus caroli</i>, <i>Mus pahari</i> and <i>Mus
spicilegus</i>. Additionally, we have computed a LastZ alignment of <i>Mus
spretus</i> and the three additional <i>Mus</i> species against the <i>Mus
musculus</i> reference genome.</p>

<p>We provide two sets of gene-trees and orthologues in Ensembl. The standard gene-trees and orthologues comprise genes from one representative for every Ensembl species, whilst the Murinae-specific gene-trees and orthologues comprise genes from all mouse strains and include genes from <i>Mus musculus</i>, <i>Mus spretus</i> and <i>Rattus norvegicus</i>. A stepwise approach via one these three species is required in order to compare genes from mouse strains to genes from species not in the Murinae set.</p>
<p>We provide multiple sets of gene-trees and orthologues in Ensembl, two of
which include genes from a mouse genome. The standard gene-trees and
orthologues comprise genes from representatives of selected Ensembl species,
whilst the Murinae-specific gene-trees and orthologues comprise genes from
all mouse strains and include genes from <i>Mus musculus</i>, <i>Rattus
norvegicus</i>, <i>Mus spretus</i> and the three aforementioned <i>Mus</i>
species. A stepwise approach via one of these six species is required in
order to compare genes from mouse strains to genes from species not in the
Murinae set.</p>

<p>In accordance with the <a href="https://en.wikipedia.org/wiki/Fort_Lauderdale_Agreement">Fort Lauderdale Agreement</a>, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.</p>
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