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 Software

SATIVA: Semi-Automatic Taxonomy Improvement and Validation Algorithm.

The tool identifies taxonomically mislabeled sequences and suggests corrections using the EPA (Evolutionary Placement Algorithm).

For more details, please visit the SATIVA page. genesis

genesis: toolkit, mainly for analyzing placements from the EPA.

A toolkit for working with phylogenetic data, mainly for evolutionary placements of short NGS reads on a reference phylogenetic tree. The library supports data in .jplace format and their visualization. It also offers some basic methods to work with trees and sequences.

For more details, please visit the genesis page.

ForeSeqs: Forecasting sequences

Tool for rrediction of missing sequences and branch lengths on phylogenies inferred using MSAs that have missing/gappy data.

For more details, please visit the ForeSeqs page.

RAxML

The latest version of RAxML can be found at Alexis github repository.

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

There is finally a new manual available for RAxML version 8.1.X. You can get it 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. Frederic Mahe, Colomban de Vargas, David Bass, Lucas Czech, Alexandros Stamatakis, Enrique Lara, Jordan Mayor, John Bunge, Sarah Sernaker, Tobias Siemensmeyer, Isabelle Trautmann, Sarah Romac, Cedric Berney, Alexey Kozlov, Edward Mitchell, Christophe Seppey, David Singer, Elianne Egge, Rainer Wirth, Gabriel Trueba, Micah Dunthorn: "Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites". BioRxiv, 050997, 2016 open access.
  2. Alexey M Kozlov, Jiajie Zhang, Pelin Yilmaz, Frank Oliver Glöckner, Alexandros Stamatakis: "Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences". BioRxiv, 042200, 2016, open access.
  3. Michael Hoff, Stefan Peter Orf, Benedikt Johannes Riehm, Diego Darriba, Alexandros Stamatakis: "Does the choice of nucleotide substitution models matter topologically?". BioRxiv, 041566, 2016, open access. Also published in BMC Bioinformatics open access.
  4. Diego Darriba, Michael Weiß, Alexandros Stamatakis: "Prediction of Missing Sequences and Branch Lengths in Phylogenomic Data". Bioinformatics, 2016, advance on-line access.
  5. Kassian Kobert, Alexandros Stamatakis, Tomas Flouri: "Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations". BioRxiv, 035873, 2016 open access.
All publications >>