Show threadMarc Robinson-RechaviJul 26, 2023
If you too like #opsin evolution, check our new #bioinformatics tool #Matreex to visualize the evolution of complex gene families, illustrated by the evolution of vertebrate red-sensitive visual opsins https://www.biorxiv.org/content/10.1101/2023.02.18.529053v1.full #SMBE2023
Marc Robinson-RechaviFeb 26, 2023
Curious to compare engagement between my Mastodon post about #Matreex and the tweet of Christophe Dessimoz over at blue-bird. So far similar (more likes at Twitter, more reposts here), but replies only here.
https://ecoevo.social/@marcrr/109930059951239969
https://twitter.com/cdessimoz/status/1629763935472701441
Marc Robinson-Rechavi (@[email protected])

Attached: 1 image 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 1/thread

ecoevo.social
Show threadMarc Robinson-RechaviFeb 26, 2023
#Matreex is available at https://github.com/DessimozLab/matreex #opensource #bioinformatics #phylogenomics #SIB
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GitHub - DessimozLab/matreex

Contribute to DessimozLab/matreex development by creating an account on GitHub.

GitHub
Show threadMarc Robinson-RechaviFeb 26, 2023
#Matreex can also be used for research into gene family evolution, providing a rapid and efficient overview of the gene family over many species. Visualization of intraflagellar transport gene families allowed us to discover complete loss in the #mixozoan Thelohanellus kitauei. #MolecularEvolution
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Show threadMarc Robinson-RechaviFeb 26, 2023
#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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Show threadMarc Robinson-RechaviFeb 26, 2023
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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Marc Robinson-RechaviFeb 26, 2023
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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