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.

2021 summer school on computational molecular evolution

Applications are now closed for the 12th summer school on computational molecular evolution organized by Ziheng Yang, Cilia Antoniou, Adam Leache and Alexis Stamatakis. It will be held once again at the Hellenic Center for Marine Research near Heraklion, Crete, Greece. The course was originally supposed to take place in May 2020.

See the course page for further details

New Software

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.

Complete re-design of Evolutionary Placement Algorithm

This is a completely re-designed version of our Evolutionary Placement Algorithm. It is at least 6 times faster than pplacer/EPA and has substantially improved parallel scalability.

It is available for download here

As before EPA-NG user support will be provided via the raxml google group.

All software >>

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

  1. Benoit Morel, Paul Schade, Sarah Lutteropp, Tom A. Williams, Gergely J. Szöllösi, Alexandros Stamatakis, "SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss", 2021, Preprint at bioRxiv
  2. Aurélien Miralles, Jacques Ducasse, Sophie Brouillet, Tomas Flouri, Tomochika Fujisawa, Paschalia Kapli, L. Lacey Knowles, Sangeeta Kumari, Alexandros Stamatakis, Jeet Sukumaran, Sarah Lutteropp, Miguel Vences, Nicolas Puillandre. "SPART, a versatile and standardized data exchange format for species partition information", 2021, Preprint at bioRxiv
  3. Emma B. Hodcroft, Nicola De Maio, Rob Lanfear, Duncan R. MacCannell, Bui Quang Minh, Heiko A. Schmidt, Alexandros Stamatakis, Nick Goldman, Christophe Dessimoz. "Want to track pandemic variants faster? Fix the bioinformatics bottleneck", 2021 Nature 591, 30-33, on-line version
  4. Nikolaos Psonis, Aglaia Antoniou, Emmanouela Karameta, Diego Darriba, Alexandros Stamatakis, Petros Lymberakis, Nikos Poulakakis. "The wall lizards of the Balkan peninsula: tackling questions at the interphase of phylogenomics and population genomics", 2021, Molecular Phylogenetics and Evolution, on-line version.
  5. Lukas Hübner, Alexey M. Kozlov, Demian Hespe, Peter Sanders, Alexandros Stamatakis. "Exploring Parallel MPI Fault Tolerance Mechanisms for Phylogenetic Inference with RAxML-NG", 2021, Preprint at bioRxiv
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.