Alexis Stamatakis

The abstract submission deadline for the 2026 Mathematical and Computational Evolutionary Biology Meeting on Crete mceb2026.sciencesconf.org has been extended until February 6

The abstract submission deadline (Jan 31st) for the 2026 Mathematical and Computational Evolutionary Biology Meeting on Crete mceb2026.sciencesconf.org is this Saturday!

The submission deadline (Jan 31st) for the 2026 Mathematical and Computational Evolutionary Biology Meeting in Crete mceb2026.sciencesconf.org is getting closer!

The submission deadline (Jan 31st) for the 2026 Mathematical and Computational Evolutionary Biology Meeting in Crete mceb2026.sciencesconf.org is getting closer!

Our raxtax tool for taxonomic classification is published: it is 2.7–100 times faster than competing tools but equally accurate - raxtax has increasing speedups with growing query and reference sequence numbers compared to existing tools: academic.oup.com/bioinformati...

Permanent Research Group Leader Position, Crete, Greece: Interested to assume long-term responsibilities for the Biodiversity Computing Group www.biocomp.gr I have set up in Crete? Apply now via apella.minedu.gov.gr/en/node/5998 (PDF also in English) - for questions email to stamatak@ics.forth.gr

Join us in Crete in May 2026 for the Mathematical and Computational Evolutionary Biology Meeting mceb2026.sciencesconf.org on the island's northern coastline near Heraklion. Abstract Deadline: January 31st

bigrig: A range simulator for the DEC[+J] model Quality software tools for science are, as a necessity, rigorously tested and verified. However, there is a major challenge to testing software used for phylogenetics and similar analysis. There is a ...

As computer scientist, I am very excited about our new biogeography simulator: bigrig - my PostDoc Ben Bettisworth implemented two algoritmically totally distinct simulators from scratch to conduct statistical tests for showing that bigrig is correctly implemented: www.biorxiv.org/content/10.1...

Join us in Crete in May 2026 for the Mathematical and Computational Evolutionary Biology Meeting mceb2026.sciencesconf.org on the island's northern coastline near Heraklion.

October 17 is your last chance to register for the 2nd conference on Machine Learning for Evolutionary Genomics Data (Dec 8-12), in the French Alps at legend2025.sciencesconf.org
The conference talks are online at legend2025.sciencesconf.org/data/book_le...

A Systematic Investigation of Overfitting in Maximum Likelihood Phylogenetic Inference Maximum Likelihood (ML) tree inference reconstructs phylogenies from Multiple Sequence Alignments (MSAs). Since MSAs are inherently noisy, ML tools may experience overfitting, whereby the inferred top...

New preprint: ML tree inference tools such as IQ-Tree and RAxML-NG do typically not overfit the data during tree searches: www.biorxiv.org/content/10.1...

Want to spend time in the French Alps and talk about Machine Learning for Evolutionary Genomics Data? Join us for the 2nd Legend conference - abstract submission deadline is on September 22 legend2025.sciencesconf.org

Do you fancy spending some days in the French Alps in December and talk about Machine Learning for Evolutionary Genomics Data? Join us for the 2nd Legend conference: legend2025.sciencesconf.org

Bit-Reproducible Phylogenetic Tree Inference under Varying Core-Counts via Reproducible Parallel Reduction Operators Motivation: Phylogenetic trees describe the evolutionary history among biological species based on their genomic data. Maximum Likelihood (ML) based phylogenetic inference tools search for the tree and evolutionary model that best explain the observed genomic data. Given the independence of likelihood score calculations between different genomic sites, parallel computation is commonly deployed. This is followed by a parallel summation over the per-site scores to obtain the overall likelihood score of the tree. However, basic arithmetic operations on IEEE 754 floating-point numbers, such as addition and multiplication, inherently introduce rounding errors. Consequently, the order by which floating-point operations are executed affects the exact resulting likelihood value since these operations are not associative. Moreover, parallel reduction algorithms in numerical codes re-associate operations as a function of the core count and cluster network topology, inducing different round-off errors. These low-level deviations can cause heuristic searches to diverge and induce high-level result discrepancies (e.g., yield topologically distinct phylogenies). This effect has also been observed in multiple scientific fields, beyond phylogenetics. Results: We observe that varying the degree of parallelism results in diverging phylogenetic tree searches (high level results) for over 31 % out of 10 130 empirical datasets. More importantly, 8 % of these diverging datasets yield trees that are statistically significantly worse than the best known ML tree for the dataset (AU-test, p < 0.05). To alleviate this, we develop a variant of the widely used phylogenetic inference tool RAxML-NG, which does yield bit-reproducible results under varying core-counts, with a slowdown of only 0 to 12.7 % (median 0.8 %) on up to 768 cores. We further introduce the ReproRed reduction algorithm, which yields bit-identical results under varying core-counts, by maintaining a fixed operation order that is independent of the communication pattern. ReproRed is thus applicable to all associative reduction operations – in contrast to competitors, which are confined to summation. Our ReproRed reduction algorithm only exchanges the theoretical minimum number of messages, overlaps communication with computation, and utilizes fast base-cases for local reductions. ReproRed is able to all-reduce (via a subsequent broadcast) 4.1 · 106 operands across 48 to 768 cores in 19.7 to 48.61 µs, thereby exhibiting a slowdown of 13 to 93 % over a non-reproducible all-reduce algorithm. ReproRed outperforms the state-of-the-art reproducible all-reduction algorithm ReproBLAS (offers summation only) beyond 10 000 elements per core. In summary, we re-assess non-reproducibility in parallel phylogenetic inference, present the first bit-reproducible parallel phylogenetic inference tool, as well as introduce a general algorithm and open-source code for conducting reproducible associative parallel reduction operations. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 882500 European Union, https://ror.org/019w4f821, 101087081

Check out our new preprint on reproducible parallel phylogenetic inference under varying core counts - it also includes a generic method for reproducible parallel associative reduction operations www.biorxiv.org/content/10.1...

Release RAxML-NG v2.0-beta2 · amkozlov/raxml-ng Main new features Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024) Multiple fast branch support measures Integrated model testing Full Changelog: 1.2.2...2.0-beta2

RAxML-NG v2.0 beta is here

github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...

Are you looking for a good excuse to visit Crete? Join us for the EMBO satellite workshop on Biodiversity Genomics - register for free via forms.gle/GRvPxCp2TnYd... limited spots available first-come first-served

raxtax: A k-mer-based non-Bayesian Taxonomic Classifier Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) to a specific lineage using a reference database that contains named seq...

Check out raxtax, our new open-source tool for taxonomic classification of barcoding sequences, it's 2.7-1000 times faster than competing tools and also implements fancy uncertainty scores: www.biorxiv.org/content/10.1...

Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data AbstractMotivation. Genotype datasets typically contain a large number of single nucleotide polymorphisms for a comparatively small number of individuals.

Are you analyzing genotype data via PCA or MDS, in particular including ancient DNA samples? Here is a novel easy-to-use tool to assess the stability of these analyses by bootstrapping the SNPs: academic.oup.com/bioinformati...

The next edition of our LEGEND conference on Machine Learning for Evolutionary Genomics Data will take place in Aussois (French Alps) from Dec 8-12 2025.

All practical information and a list of our keynote speakers are available at: legend2025.sciencesconf.org

We hope to meet you there again!

YouTube video by Alexandros Stamatakis The EcoFreq Tool - compute with cleaner & cheaper energy

By dynamic CPU clock frequency scaling our EcoFreq tool reduces your energy consumption and CO2 footprint by 15-18% while only experiencing a 10% throughput decrease. The tool is free of charge for academic use.

A short video explaining EcoFreq: youtu.be/cpw--Tsbib4

Μετά το brain - drain η Ελλάδα βιώνει και τη διαρροή δειγμάτων για επιστημονική έρευνα - Dnews Παρότι αρκετές ελληνικές επιστημονικές ομάδες θα μπορούσαν να ηγηθούν ερευνητικών έργων λόγω του πλούτου των αρχαιολογικών και παλαιοντολογικών δειγμάτων της χώρας, συχνά περιορίζονται στον ρόλο του σ...

News article about the phenomenon of specimen-drain from the global South to the global North by award-winning science journalist and good friend Vasiliki Michopoulou - on 3 out of 35 ancient DNA papers with Greek samples, Greek scientists were first and/or last authors
www.dnews.gr/eidhseis/sci...

Another new term we invented together with a colleague is specimen-drain: the export of valuable biodiversity, ancient DNA, or other samples to countries of the global North that have money to process them coupled with losing the lead on the respective research papers

Frontiers | Necessary reforms in the Greek academic system

"To yield Greece more competitive, substantial increases of R&D expenditure and a long term strategic development plan are required such that the country becomes more than a tourist destination in the European periphery." - see our policy paper for more: www.frontiersin.org/journals/pol...

Computational Molecular Evolution The need for effective and informed analysis of biological data is increasing with the explosive growth of genomic data. A phylogenetic framework is central to many molecular evolutionary approaches …

Last reminder - applications for our 2025 school on computational molecular evolution in Crete close in one week - there will be no application deadline extensions.
meetings.embo.org/event/25-com...

Computational Molecular Evolution The need for effective and informed analysis of biological data is increasing with the explosive growth of genomic data. A phylogenetic framework is central to many molecular evolutionary approaches …

Applications are still open for our 2025 school on computational molecular evolution in Crete, the application deadline is November 1st - only about 10 days from now.
meetings.embo.org/event/25-com...

Predicting Phylogenetic Bootstrap Values via Machine Learning Abstract. Estimating the statistical robustness of the inferred tree(s) constitutes an integral part of most phylogenetic analyses. Commonly, one computes

Do you want to rapidly predict bootstrap values via machine learning? You can now use our Educated Bootstrap Guesser: academic.oup.com/mbe/advance-...

Before somebody else comes up with it, here is a new term I invented: brain-redrain

Definition: brains that return to their underdeveloped home country in the hope to help improving things but then leave again since they are frustrated because nothing will ever change there.

Computational Molecular Evolution The need for effective and informed analysis of biological data is increasing with the explosive growth of genomic data. A phylogenetic framework is central to many molecular evolutionary approaches …

applications are still open for our 2025 school on computational molecular evolution in Crete, the application deadline is November 1st - about 3 weeks from now. meetings.embo.org/event/25-com...

Computational Molecular Evolution The need for effective and informed analysis of biological data is increasing with the explosive growth of genomic data. A phylogenetic framework is central to many molecular evolutionary approaches …

Registrations are open for the 2025 school on computational molecular evolution in Crete, the application deadline is November 1st.
meetings.embo.org/event/25-com...

Computational Molecular Evolution The need for effective and informed analysis of biological data is increasing with the explosive growth of genomic data. A phylogenetic framework is central to many molecular evolutionary approaches …

Registrations are open for the 2025 school on computational molecular evolution in Crete: meetings.embo.org/event/25-com...