The Exelixis Lab


Enabling Research in Evolutionary Biology

Our Mission - Enable Research in Evolutionary Biology

Our focus is on the evolution of hardware and parallel computer architectures as well as on the evolution of molecular sequences.

We understand Bioinformatics as a discipline that develops algorithms, models, and tools that help Biologists to generate new biological insights and knowledge. We try to bridge the gap between the world of systematics and the world of high performance computing.

Due to the increasing descrepancy between the pace of molecular data accumulation and increase in CPU speeds (which is much slower), which we call the "Bio-Gap" we feel that the time has come to establish parallel computing as standard technique in Bioinformatics.

NEW SISTER LAB in CRETE - Join the Biodiversity Computing Group (BCG)

As of 2023 Alexis will establish a new research group called Biodiversity Computing Group (BCG) at the Institute of Computer Science of the Foundation for Research and Technology Hellas in Heraklion, Crete, Greece.

The new group is funded through an EU ERA chair project for a duration of five years and will closely collaborate with his existing research group in Heidelberg.

We will soon start hiring, there are 4 PhD and 2 PostDoc positions available. We will pay competitive salaries (80% of HITS salaries, i.e., difference of cost of living between Germany and Greece) including health and social insurance at all levels (PhD students, PostDocs, PI). We are looking for computer scientists, Bioinformaticians, and "programming Biologists" to fill these positions. If you are interested to work where other people go on vacations and wish to be notified once the application process opens please send an email to Alexis.

Check the Press Release

13th Summer School on Computational Molecular Evolution

Applications now open

Applications for the 13th summer school on computational molecular evolution organized by Cilia Antoniou, Ziheng Yang, Adam Leache, and Alexandros Stamatakis from May 7-18 2023, in Crete, Greece are now open at the following link

New Research Area

Ancient DNA research

Alexis was recently appointed as Affiliated Scientist at the Evolutionary Genetics and Paleogenomics (EGP) lab of the Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, in Heraklion, Crete, Greece. The lab mostly focuses on ancient DNA analysis and you can find the web-page here.

The connection to this research lab in Crete offers opportunities to conduct data analysis projects in the framework of Bachelor/Master theses for KIT students abroad.

New Software

Lagrange-NG

Attention Biogeographers! We just released Lagrange-NG, a re-design of the popular Lagrange tool: it's faster, runs in parallel, and has better code quality:

It is available for download here

SoftWipe

A tool and benchmark for assessing adherence of scientific software to coding quality standards.

It is available for download here.

NetRAX

A tool for accurate and fast maximum likelihood based inference of phylogenetic networks.

It is available for download here.

SpeciesRax

A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss.

It is available for download here.

SCRAPP

Species Counting on Reference trees viA Phylogenetic Placements - bridging the gap between phylogenetic placement results and alpha diversity metrics, with the possibility of further in-depth analysis.

It is available for download here

RootDigger

RootDigger uses a non-reversible Markov model to compute the most likely root location on a given tree.

It is available for download here

GeneRax: Species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss

Our first tool for gene tree species tree reconciliation. Open-source code is available here, a respective preprint can be found here.

ParGenes: massively parallel inference of gene trees

A tool for massively parallel model selection and phylogenetic tree inference on thousands of genes using thousands of cores, based on ModelTest-NG and RAxML-NG. Now published in Bionformatics and available for download here.

RAxML-NG Web-Server

The brand new web-server for the completely re-designed version of RAxML, called RAxML-NG is available here.

RAxML-NG

The latest version of RAxML-NG, the complete re-design of RAxML can be found at Alexey's github repository.

RAxML questions, help & bug reports: please use the RAxML google group

The respective paper can be found here

Students from KIT

We are always looking for student programmers (HiWis) and students interested in doing bachelor/master theses projects with us. If you are interested please send an email to Alexis at Alexandros dot Stamatakis at h hyphen its dot org

New Papers

Our 5 Most Recent Papers/Preprints

  1. Dimitri Hoehler, Julia Haag, Alexey M. Kozlov, Alexandros Stamatakis, "A representative Performance Assessment of Maximum Likelihood based Phylogenetic Inference Tools", preprint at bioRxiv
  2. Julia Haag, Lukas Hübner, Alexey M Kozlov, Alexandros Stamatakis, "The Free Lunch is not over yet - Systematic Exploration of Numerical Thresholds in Phylogenetic Inference", preprint at bioRxiv
  3. Julia Haag, Dimitri Hoehler, Ben Bettisworth, Alexandros Stamatakis, "From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses", preprint at bioRxiv
  4. Ben Bettisworth, Stephen A. Smith, Alexandros Stamatakis, "Lagrange-NG: The next generation of Lagrange", preprint at bioRxiv
  5. Demian Hespe, Lukas Hübner, Peter Sanders, Alexandros Stamatakis, "ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms", preprint at arXiv
All publications >>

Collaborative Project with Cyprus

Eco-evolutionary dynamics on Cyprus: a multitaxon approach to population differentiation within an isolated island

We are participating at this joint research project with colleagues from Cyprus and Greece. For further information please visit the project website.