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

legend2024 : Machine Learning for Evolutionary Genomics Data - Heraklion (May 13-15)

Together with colleagues from abroad I am organizing this conference at FORTH in Crete. Please consult the legend2024 conferenace web-site for all details.

Abstract submission deadline: February 21st, 2023

New Software

Pythia

A tool to predict the difficulty of phylogenetic analysis of Multiple Sequence Alignments (MSA).

It is available for download here

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:

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. Nikolaos Psonis, Despoina Vassou, Argyro Nafplioti, Eugenia Tabakaki, Pavlos Pavlidis, Alexandros Stamatakis, Nikos Poulakakis, "Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes", preprint
  2. Benoit Morel, Tom A. Williams, Alexandros Stamatakis, Gergely J. Szollos, "AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer and loss", preprint at bioRxiv
  3. Isabelle Ewers, Lubomír Rajter, Lucas Czech, Frédéric Mahé, Alexandros Stamatakis, Micah Dunthorn, "Interpreting phylogenetic placements for taxonomic assignment of environmental DNA", Journal of Eukaryotic Microbiology, open access
  4. Johanna Trost, Julia Haag, Dimitri Hoehler, Laurent Jacob, Alexandros Stamatakis, Bastien Boussau, "Simulations of sequence evolution: how (un)realistic they are and why", preprint at bioRxiv
  5. Anastasis Togkousidis, Olga Chernomor, Alexandros Stamatakis, "Parallel Inference of Phylogenetic Stands with Gentrius", accepted for publication at HiCOMB 2023.
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.