Marc Robinson-Rechavi<p>If you too like <a href="https://ecoevo.social/tags/opsin" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>opsin</span></a> evolution, check our new <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> tool <a href="https://ecoevo.social/tags/Matreex" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Matreex</span></a> to visualize the evolution of complex gene families, illustrated by the evolution of vertebrate red-sensitive visual opsins <a href="https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1.full" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">23.02.18.529053v1.full</span></a> <a href="https://ecoevo.social/tags/SMBE2023" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SMBE2023</span></a></p>
#matreex
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#Matreex can be used for teaching, as here with the classical example of opsin evolution: notice the parallel loss of blue- and green-sensitive opsins in snakes and mammals, the duplications in frugivorous old-world primates, and the duplications and losses in fishes according to habitat. #opsin #MolecularEvolution
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In #Matreex, we dynamically show the "phylogenetic profile" of collapsed subtrees, allowing both a manageable size of the gene tree (through collapsing of subtrees) and information about the subtrees (through phylogenetic profiles).
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New preprint, by Victor Rossier with the group of Christophe Dessimoz (#UNIL and #SIB), introducing #Matreex, a new dynamic tool to scale-up the visualisation of gene families, and its application to showing loss of intraflagellar transport in a myxozoan
https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1
#phylogeny #phylogenomics #bioinformatics #BigData #visualization #vizbi #myxozoan @dee_unil
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