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Alexei Drummond

@alexeidrummond.bsky.social
2.2K followers 2.1K following 14 posts

Professor of Computational Biology, University of Auckland. Atheist, Rock climber, Trail runner. Co-creator of BEAST1 and BEAST2. Founder of Geneious.

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Alexei Drummond @alexeidrummond.bsky.social · 28/07/2026
Get excited :) PhyloSpec is coming! A shared standard + modelling language for phylogenetic models. Write a model once, run it across engines like BEAST X, BEAST 2.8 & RevBayes. Easy and reproducible. Built by @tochsner.bsky.social & collaborators (ETH Zürich, Auckland, LMU). phylospec.com
phylospec.com
PhyloSpec
A standardized way to describe phylogenetic model components, common assumptions, and best practices in the field of phylogenetics.
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Molecular Biology and Evolution @molbioevol.bsky.social · 16/12/2025
To address uncertainty in model choice for reconstructing population history, Xu, @alexeidrummond.bsky.social et al. introduce a new Bayesian model averaging (BMA) framework. 🔗 doi.org/10.1093/molbev/msaf297 #evobio #molbio #compbio
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Molecular Biology and Evolution @molbioevol.bsky.social · 07/07/2026
Klawitter & @alexeidrummond.bsky.social introduce novel and efficient methods for estimating the credible level of individual tree topologies using tractable tree distributions, specifically conditional clade distribution (CCD). 🔗 doi.org/10.1093/molbev/msag141 #societyjournal #compbio
doi.org
Bayesian credible sets for phylogenetic tree topologies with applications to coverage analysis and cross-model comparison
Abstract. Credible intervals and credible sets, such as highest posterior density intervals, form an integral statistical tool in Bayesian phylogenetics, b
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Alexei Drummond @alexeidrummond.bsky.social · 28/07/2026
I encourage independent Wikipedia editors with an interest in phylogenetics to review my Draft of the StarBEAST software page. Obviously I have a conflict of interest as an author on the first two versions of this software. I have stated that clearly in the Talk :) en.wikipedia.org/wiki/Draft:S...
en.wikipedia.org
Draft:StarBEAST - Wikipedia
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Molecular Biology and Evolution @molbioevol.bsky.social · 17/06/2025
Vaughan & @tanjastadler.bsky.social develop a method to infer multitype population trajectories and apply it to MERS-CoV, revealing transmission patterns between camels and humans. 🔗 doi.org/10.1093/molbev/msaf130 #evobio #molbio #virus
doi.org
Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data
Abstract. Phylodynamic methods provide a coherent framework for the inference of population parameters directly from genetic data. They are an important to
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 02/07/2025
BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be... Details and instructions for installing on the BEAST website: beast.community
The BEAST X logo - an octopus wrapping its noodley appendages round the letter X.
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Clare I. M. Adams @clare-edna.bsky.social · 09/07/2025
@alexeidrummond.bsky.social gave a wonderful keynote at @geneticsaus.bsky.social about how Bayesian/MCMC #models can be used on #cancer cells to determine when they originated and updates on #LPhy for all those #evolutionary #biologists out there.
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Alexei Drummond @alexeidrummond.bsky.social · 23/04/2025
Taming the BEAST Beijing! July 14th-18th 2025 Register now :) Application deadline 25th April. taming-the-beast.org/workshops/Ta...
taming-the-beast.org
Taming the BEAST Beijing
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Alexei Drummond @alexeidrummond.bsky.social · 14/02/2025
Check out our new method for summarising BEAST trees. The CCD0-MAP tree gives much more accurate results than MCC tree. It returns the tree that maximises the product of sampled clade probabilities regardless of whether that tree was sampled. Highly recommend :) journals.plos.org/ploscompbiol...
journals.plos.org
Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities
Author summary Our research introduces novel methods to analyse a set of phylogenetic tree topologies, such as those generated by Bayesian Markov Chain Monte Carlo algorithms. We define a new model fo...
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David Pollock @genomesevolve.bsky.social · 10/01/2025
Looks like another nice example of convergence helping to identify (not so nice for us) adaptation.
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Peter Gleick @petergleick.bsky.social · 25/12/2024
If you've never donated to Wikipedia, now's the time. Elon Musk is attacking it because it's one of the only sources of honest, curated information that he can't control. www.newsweek.com/elon-musk-ta...
newsweek.com
Elon Musk takes aim at Wikipedia
The billionaire has become one of the most prominent supporters of President-elect Donald Trump.
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Alex Mackintosh @thymelicus.bsky.social · 12/12/2024
My and Derek Setter's work on gene flow is now published in the latest issue of Genetics. We show that it is possible to detect past gene flow between two populations by summarising the asymmetry in pop-specific external branch lengths. 1/2 tinyurl.com/5ff8ch9e
tinyurl.com
Genealogical asymmetry under the isolation with migration model and a two-taxon test for gene flow
Abstract. Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the A
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 10/12/2024
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X www.biorxiv.org/content/10.1101/202…
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Ben Moore @bentm.bsky.social · 05/12/2024
20%, under $15m, of Marsden funding went to social sciences while just under $60m went to hard sciences. Total govt research funding in year to March 2023 was ~$1.1b (0.29% of GDP). Cutting the humanities out of Marsden is just spite.
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Nicola Gaston @nicgaston.bsky.social · 05/12/2024
My slightly more considered take on the Marsden fund changes is now here. This govt is focused on the impacts of funding — I don’t mind that — but they don’t seem to have thought for a second about the impact of the lack of it. On people; on society; on academic freedom.
theconversation.com
Funding research for economic return sounds good – but that’s not how science really works
The Marsden Fund was set up to support pure research. Diverting half of it to fund applied research undermines New Zealand’s potential to generate ideas that underpin commercial success.
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Simon Dellicour @sdellicour.bsky.social · 04/12/2024
How fast are viruses spreading in the wild? Check out our latest study now published in @plosbiology.bsky.social: doi.org/10.1371/jour.... A study performed with Paul Bastide, Pauline Rocu, Denis Fargette, Olivier Hardy, @msuchard.bsky.social, @stephaneguindon.bsky.social, and Philippe Lemey (1/7)
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Paul Gardner @ppgardne.bsky.social · 05/12/2024
Is this the shortest term thinking government NZ has ever had? Cut hospitals, cut ferries, cut R&D, cut universities, ... Is it all ignorance + arrogance, or do they think their rapture is coming? What is going on???
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Harald Ringbauer @hringbauer.bsky.social · 03/12/2024
PhD opportunity in computational population genetics at @MPI_EVA_Leipzig: Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬 Please spread the word! 📢🙌 #aDNA #PopGen www.eva.mpg.de/de/karriere/...
Sketch of IBD segments linking Medieval genomes from the Black Death (1350 CE) to modern Europeans. Logo of ERC-funded research.
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Altmetric @altmetric.com · 03/12/2024
One of the reasons Bluesky is seeing more engagement: other platforms have adopted the behaviour of de-prioritising external links (like, say, to research papers) due to Ad models. See this: bsky.app/profile/alt... Here links can be freely shared without being drowned out or de-emphasized
bsky.app
@altmetric.com on Bluesky
We’re no experts but this sounds like it might be suboptimal for disseminating research. [contains quote post or other embedded content]
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Diego Ortega-Del Vecchyo @delvecchyo.bsky.social · 02/12/2024
Don't forget to submit your abstract for "Probabilistic Modeling in Genomics 2025". Deadline: January 10th, 2025. meetings.cshl.edu/meetings.asp...
meetings.cshl.edu
Probabilistic Modeling in Genomics
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
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Stephane Guindon @stephaneguindon.bsky.social · 02/12/2024
Modeling the velocity of evolving lineages and predicting dispersal patterns www.pnas.org/doi/10.1073/...
pnas.org
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Altmetric @altmetric.com · 03/12/2024
There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research. A Place of Joy.
‘A place of joy’: why scientists are joining the rush to Bluesky
Researchers say the social-media platform — an alternative to X — offers more control over the content they see and the people they engage with.: https://www.nature.com/articles/d41586-024-03784-6
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Alexei Drummond @alexeidrummond.bsky.social · 26/11/2024
Agree. I usually get good value out of reviewers comments, especially from top specialist journals (Systematic Biology, Molecular Biology and Evolution, PLoS Comp Bio etc).
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Rob Lanfear @roblanfear.bsky.social · 26/11/2024
My experience (in phylogenetics, not deep learning) is almost the opposite. When I ask colleagues I know well to look at something, most are polite and encouraging but not *all that critical or useful*. But when I get peer reviews back, they are _almost_ always critical, constructive, and useful.
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Jonathan Pritchard @jkpritch.bsky.social · 22/11/2024
In a new preprint led by @TheNikhilMilind, we explored a fascinating paradox: For many traits the number of duplications or loss-of-function (LoF) mutations is correlated with phenotype. Curiously, for most traits, the AVERAGE direction of LoFs and Dups is the SAME. Why?
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Alexei Drummond @alexeidrummond.bsky.social · 19/11/2024
This paper suggests some other directions: pubmed.ncbi.nlm.nih.gov/38916476/
pubmed.ncbi.nlm.nih.gov
Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation - PubMed
Models have always been central to inferring molecular evolution and to reconstructing phylogenetic trees. Their use typically involves the development of a mechanistic framework reflecting our unders...
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Alexei Drummond @alexeidrummond.bsky.social · 16/11/2024
My son claims 399 and his logic seems sound.
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Deon de Jager @ddj-sa.bsky.social · 15/11/2024
Today is the 40th anniversary of the first #ancientDNA paper, ever! "DNA sequences from the quagga, an extinct member of the horse family" www.nature.com/articles/312.... The quagga was a subspecies of plains zebra endemic to #SouthAfrica (where I'm from)! #SciSky @aarc-community.bsky.social
nature.com
DNA sequences from the quagga, an extinct member of the horse family - Nature
Nature - DNA sequences from the quagga, an extinct member of the horse family
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Alexei Drummond @alexeidrummond.bsky.social · 16/11/2024
Sacred Kingfisher in NZ behaves similarly :) One of my favourite birds. I was very happy to spot a Belted Kingfisher when I was visiting Colorado earlier this year.
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Alexei Drummond @alexeidrummond.bsky.social · 14/11/2024
I would say model selection (by estimating marginal likelihood) is one of the most frustrating inference tasks in real-world Bayesian phylogenetic inference. The methods are very slow and seldom accurate. Model-averaging is one solution, when implemented. AI might indeed be another :)
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Alexei Drummond @alexeidrummond.bsky.social · 12/11/2024
Have ideas about how AI/deep-learning can augment Bayesian model-based (phylogenetic) inference in scientific software like BEAST2? I would love to hear from you. We are embarking on some exploratory work in this direction and there is a lot to learn :)
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Alexei Drummond @alexeidrummond.bsky.social · 06/11/2024
Today I was reminded that I am living in a simulation. The postdoc running things seems to be testing what happens when mendacity is turned up to maximum.
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Alexei Drummond @alexeidrummond.bsky.social · 21/10/2024
Last chance to fill in our survey! Have your say while you can :) Thanks for all those of you that already have!
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Alexei Drummond @alexeidrummond.bsky.social · 20/09/2024
Want to have your say about BEAST2 future developments? Fill in our BEAST2 user and developer survey :) forms.gle/mTWvaXHZAA12...
forms.gle
BEAST 2 user and developer experience and future development survey
This survey aims to gather feedback from the BEAST2 user and developer community to inform the development of future versions of BEAST. Your insights will help us prioritise features, address pain poi...
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Alexei Drummond @alexeidrummond.bsky.social · 15/08/2024
Hello Bluesky people :)
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