#phylogenetics — Public Fediverse posts

Pipeline release! nf-core/phyloplace v2.1.0 - v2.1.0 - 2026-08-03!
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.1.0

#evolution #evolutionarytree #phylogeneticplacement #phylogenetics #sequenceclassification #taxonomyassignment #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/phyloplace v2.0.1 - Documentation improvements, software updates!
nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.0.1

#evolution #evolutionarytree #phylogeneticplacement #phylogenetics #sequenceclassification #taxonomyassignment #nfcore #openscience #nextflow #bioinformatics

Hey IQTree3 paper is out. Bread and butter for tree building anything in my workflow. They have a pretty standout documentation too.

#bioinformatics #phylogenetics

https://academic.oup.com/mbe/article/43/5/msag117/8669857

New paper: "The Tree and Its Echo" — ultrametric organization from pre-numeric first principles.

Before numbers: marks on a bone. Three primitives: correspondence, order, nesting. Hierarchy without metrics.

The independence assumption is the fallacy. Baseline convergence: similarity is the default, not the exception. Tree = residual. P0 PASSED (p<0.001).

DOI: 10.5281/zenodo.20348370

#Mathematics #Physics #ComplexSystems #SpinGlasses #Ultrametric #Phylogenetics #Science

Predictable evolution is bad news for toads, good news for their predators

"Under certain circumstances, the process of evolution can be highly predictable, especially when there are limited solutions to a particular problem, such as resistance to dangerous toxins"

#SciComm by @GrrlScientist

#evolution #poisons #phylogenetics #Australia https://grrlscientist.medium.com/predictable-evolution-is-bad-news-for-toads-good-news-for-their-predators-7260c33dc54c

Predictable evolution is bad news for toads, good news for their predators

"Under certain circumstances, the process of evolution can be highly predictable, especially when there are limited solutions to a particular problem, such as resistance to dangerous toxins"

#SciComm by @grrlscientist

#evolution #poisons #phylogenetics #Australia https://grrlscientist.medium.com/predictable-evolution-is-bad-news-for-toads-good-news-for-their-predators-7260c33dc54c

MBE is excited to launch our newest Call for Papers on the Major Transitions of Life, covering all aspects of phylogenomic research.

🔗 academic.oup.com/mbe/pages/call-for-papers-on-the-major-transitions-of-life

Guest Editors:
Davide Pisani
Anja Spang

Accepted manuscripts will receive a 20% discount on the APCs, on top of the SMBE membership discount.

Toward a genomic understanding of the tree of life
🔗 https://doi.org/10.1093/molbev/msag043

#evobio #molbio #phylogenetics

RE: https://mastodon.green/@plazi_species/116260383338896477

#Endemic #species are always interesting from different perspectives, e.g. from an #evolutionary and #ecological point of view. This also applies to #skinks of the genus
#Madascincus, being with several known species endemic to #Madagascar.
A. Miralles et al. (2026) described based on #multilocus #phylogenetics and #morphology two #newspecies:
M. #irery and M.
#minotaurus, with restricted distributions to limited areas of Madagascar only.
© this text #StefanFWirth

Could the shape of phylogenetic trees contain hidden information? Siqi Liu, Sarah Svensson & Daniel Falush show that the "backboned" shape of the phylogenetic tree of #Klebsiella pneumoniae may reveal a history of diversifying selection on an unknown trait.
#microbiology #phylogenetics
https://plos.io/4bgI3qz

Is there something analogous to #ClintReptiles but for #botany? I want someone to explain me the #plant branch of the tree of life while telling how much they love it, clade by clade.

#systematics #treeOfLife #cladistics #phylogenetics

Fresh WIP piece of #Archaea #phylogenetics data for a collaborator.

Those barplot margins are driving me crazy - it's actually throwing off the immediate impression of the data! (pink bars are essentially all 1/2 or less of the orange bars, which is pretty important in context) I really need to buckle down and get to hand-coding my trees from scratch using #rlang or #julialang soon.

Hmm. How's Julia ecosystem for phylogenetic trees these days?

#microbiology #bioinformatics

Our first preprint of 2026 is online:

Phylogenetic based dissection of eukaryotic Mo-insertase functionality: From mechanism to complex assembly
https://doi.org/10.64898/2025.12.12.693926

#Evolution #Phylogenetics
@PuckerLab

Lineages of carnivorous mammals that established on new continents diversified faster— even before they moved into new territory. That suggests those lineages have diversified specifically because they're better competitors https://doi.org/10.1086/738413

#science #evolution #mammals #paleontology #phylogenetics

#SequenceAlignment is notoriously prone to error. Our latest #preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. https://www.biorxiv.org/content/10.64898/2025.12.01.691663v1 1/10 #MSA #alignment #phylogenetics

Sharma & Kumar present the Net Bootstrap Support (NBS) approach that accounts for phylogenetic variation in the estimates of bootstrap confidence.

🔗 https://doi.org/10.1093/molbev/msaf296

#evobio #molbio #phylogenetics

Tabatabaee et al. introduce CASTLES-Pro for estimating species tree branch lengths while accounting for both gene duplication and loss and incomplete lineage sorting.

🔗 https://doi.org/10.1093/gbe/evaf200

#genome #evolution #phylogenetics

"Clint's Reptiles | Not All Dogs Have Bones"

#Phylogenetics is Phun!

Clint's Reptiles is my new favorite #Youtube channel. It's not just #educational and informative, it's high art.

https://www.youtube.com/watch?v=YerdELZuEhY

And low art, but definitely high art. You know, self-referential, culturally aware and, but subtly so.