The new OrthoFinder paper is out now!
In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets
www.nature.com/articles/s41...
github.com/OrthoFinder/...
Professor Joe Felsenstein FRS is elected a Fellow of the Royal Society. After initially working on population genetics theory of recombination, of migration, and of speciation, his main focus has been on phylogenetic inference. #RSFellows https://royalsociety.org/people/joseph-felsenstein-38106/
Very happy to announce a big new paper from the lab, led by grad students @smishra677.bsky.social and Laia Pomar-Pallarès (in collaboration with @roblanfear.bsky.social).
We introduce a new way to study introgression, with accompanying software (DAFT)
1/n 🧵
www.biorxiv.org/content/10.6...
Wong et al. present IQ-TREE version 3, with new features including mixture models, gene and site concordance factors, integration with phylogenomic divergence time estimation, and a fully featured sequence simulator.
🔗 doi.org/10.1093/molbev/msag117
#evobio #molbio #compbio
Finally we know where the enigmatic Caribbean genus Calisto goes in the tree of life, thanks to the amazing work by Rayner Nunez! Mixture models seem to be the way to go!
doi.org/10.1111/syen...
Ok, this is cool...
Treemble:
A graphical tool to generate Newick strings from phylogenetic tree images🧪
academic.oup.com/bioinformati...
Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org.
The authors of every recent paper we have to use tools like this on should be added to a "bad at sharing data" public list.
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GABBI is available on #Github! 👇
github.com/bjzelvelder/...
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New tool for #Phylogenomics 🚀
GABBI is an open-source pipeline that designs target-capture kits using whole-genome alignments across multiple taxa instead of a single reference genome.
👉more informative loci, better phylogenetic resolution, less reference bias - even with #museum specimens! 🪲
The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.
We provide the first reliable hypothesis on the phylogenetic position of Calisto and Llorenteana within the tribe Satyrini, based on genomic data representing all subtribes.
We apply for the first t.....
Genome Alignment Based Bait Inference (GABBI): A fully automated probe design pipeline based on whole-genome alignments for target capture phylogenomics - bjzelvelder/GABBI
Ok, this is cool...
Treemble:
A graphical tool to generate Newick strings from phylogenetic tree images🧪
academic.oup.com/bioinformati...
Treemble is a native desktop application for macOS and Windows and is freely available, with documentation, at treemble.org.
Interested in #plant #herbivore #predator #symbiont interactions and #thrips #biocontrol? I am recruiting a permanent lab technician at #CBGP #Montpellier. All backgrounds and identities welcome. Please repost! @cbgpmontpellier.bsky.social
More info here:
recrutement.cirad.fr/offre-de-emp...
Rémi Allio
Rémi Allio
We are very glad to introduce a new method for designing phylogenetically informative target-enrichment datasets that leverages recent whole-genome alignment methods to identify thousands of shared and homologous regions across a broad range of reference taxa!
Please, check out Benjamin's preprint!
A new method based on genome alignments provides a highly resolutive target enrichment set for weevils (Coleoptera, Curculionoidea) https://www.biorxiv.org/content/10.64898/2026.05.09.724036v1
