Mario dos Reis

Not ready yet! Hopefully soon!

Benchmarking of software for Bayesian sampling of divergence times using genomes

We have a new Bayesian sampler of divergence times that is smoking fast! Benchmarking by the exceptional @lauramulvey.bsky.social

Pre-Christmas moleclular-clock shenanigans with @sabifo4.bsky.social @mariodosreis.bsky.social @zihengyang.bsky.social

It is #WorldAIDSDay! For this special #ScienceInContext Dr Fabricia Nascimento & Prof Sanjay Mehta join @eonore.bsky.social to speak about phylodynamic inference, HIV transmission, migration, genome sequencing & ethics
@imperialcollegeldn.bsky.social @ucsandiego.bsky.social 🧵1/2
youtu.be/SzdAhdjJuAE

Applications for the London TREES DTP programme are now open: www.trees-dla.ac.uk/news/applica...

We have a project on Bayesian phylogenetics! 😀
www.trees-dla.ac.uk/projects/int...

Michael Benton books, i.e, Extinctions, When Life Nearly Died

Maybe look in /Applications/RStudio.app/Contents/Resources/app/R/modules/SessionAutomation.R

Are you using Rstudio? If so, Rstudio startup scripts are loaded after .Rprofile is read, and so everything is overwritten. For example, if you edit Rstudio's Tools.R you can permanently set the graphics device.

I had a similar problem and I had memory access errors. Once in a while in a gigantic for loop, I was accessing vectors outside the space allocated to them. You can verify you don't have this bug by accessing all vectors with () instead of []. For example: my_vector(i).

With @anthonydemotte.bsky.social, @muthubioinfo.bsky.social, and @bqminh.bsky.social

Frustrated that MCMCtree does not have complex substitution models? The IQ-tree team has now developed IQ2MC, an interface for seamless integration of IQ-tree's substitution models with MCMCtree's fast Bayesian pipeline for clock dating. Read the preprint here: ecoevorxiv.org/repository/v...

A reminder that we have two open PhD projects on Bayesian phylogenetics in the lab:

One with the new TREE Doctoral Landscape Awards: www.trees-dla.ac.uk/projects/int... (deadline 20th Jan)

And another with CSC: www.findaphd.com/phds/project... (deadline 29th Jan)

Assessing the Adequacy of Morphological Models Using Posterior Predictive Simulations Abstract. Reconstructing the evolutionary history of different groups of organisms provides insight into how life originated and diversified on Earth. Phyl

So excited to see this paper finally published! 🥳 This was the main focus of my PhD and demonstrates the application of model adequacy for models of morphological evolution. 1/n
academic.oup.com/sysbio/advan...

We have a project on Bayesian phylogenetics: www.trees-dla.ac.uk/projects/int... with @zihengyang.bsky.social

Over 120 PhD projects have now been released as part of the new London Doctoral Landscape Awards, for start in Oct 2025. www.trees-dla.ac.uk/projects

Geometriphylogenetics xkcd.com/3010

Bayesian Selection of Relaxed-clock Models: Distinguishing Between Independent and Autocorrelated Rates In Bayesian molecular-clock dating of species divergences, rate models are used to construct the prior on the molecular evolutionary rates for branches in the phylogeny, with independent and autocorre...

It's also in bioRxiv: www.biorxiv.org/content/10.1...

Bayesian Selection of Relaxed-clock Models: Distinguishing Between Independent and Autocorrelated Rates Abstract. In Bayesian molecular-clock dating of species divergences, rate models are used to construct the prior on the molecular evolutionary rates for br

Our paper on Bayesian selection of relaxed clock models is out in Systematic Biology! This is the work of our PhD student Muthukumaran Panchaksaram, in collaboration with Lucas Freitas from Brazil.
doi.org/10.1093/sysb...

The new TREES London PhD training programming in the Environmental Sciences is now up!
www.trees-dla.ac.uk

Developing efficient Bayesian samplers for evolutionary analysis in the Tree of Life at Queen Mary University of London on FindAPhD.com PhD Project - Developing efficient Bayesian samplers for evolutionary analysis in the Tree of Life at Queen Mary University of London, listed on FindAPhD.com

PhD position available in our lab: www.findaphd.com/phds/project...