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.

2020 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.

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, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukas Hübner, Sarah Lutteropp, Dora Serdari, Evangelia-Georgia Kostaki, Ioannis Mamais, Alexey Kozlov, Pavlos Pavlidis, Dimitrios Paraskevis, Alexandros Stamatakis. "Phylogenetic analysis of SARS-CoV-2 data is difficult", bioRxiv, 08.05.239046, 2020, preprint
  2. Alexey M Kozlov, João M Alves, Alexandros Stamatakis, and David Posada. "CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data", bioRxiv, 07.31.230292, 2020 preprint.
  3. Pierre Barbera, Lucas Czech, Sarah Lutteropp, Alexandros Stamatakis. "SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements", bioRxiv, 969980, 2020 preprint.
  4. Ben Bettisworth, Alexandros Stamatakis. "RootDigger: a root placement program for phylogenetic trees", bioRxiv, 935304, 2020 preprint.
  5. David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J McCarthy, Stephanie C Hicks, Mark D Robinson, Catalina A Vallejos, Niko Beerenwinkel, Kieran R Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharin Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M Kiełbasa, Jan O Korbel, Alexey M Kozlov, Tzu-Hao Kuo, Boudewijn PF Lelieveldt, Ion I Mandoiu, John C Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Łukasz Rączkowski, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J Theis, Huan Yang, Alex Zelikovsky, Alice C McHardy, Benjamin J Raphael, Sohrab P Shah, Alexander Schönhuth, "Eleven grand challenges in single-cell data science". Genome Biol 21, 31 (2020) open access / preprint
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.