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.

2017 summer school on computational molecular evolution

Applications are now open for the 9th summer school on computational molecular evolution organized by Nick Goldman, Ziheng Yang, Cilia Antoniou, and Alexis Stamatakis. It will be held once again in Hinxton, UK.

See the course page for further details

New Software

The low-level phylogenetic likelihood library: libpll

libpll is a new library that facilitates phylogenetic analyses. Libpll is a low-level re-design of our previous PLL, that offers unprecedented flexibility when implementing new models, testing hypotheses and/or developing new tools, methods or pipelines.

Apart from the highly-optimized phylogenetic likelihood function, libpll offers the following functionality:

  • parsing of alignment file formats (FASTA/PHYLIP)
  • parsing of tree file formats (binary rooted, unrooted, n-ary trees)
  • flexibility in defining custom models of dna evolution
  • support for heterotachous and mixture models
  • support for models with arbitrary number of states
  • parsimony functions
  • support for arbitrary number of rate heterogeneity categories
  • functions for weighted parsimony
  • methods for ascertainment bias correction
  • tree visualization

Libpll is highly optimized and can make use of the SSE3/AVX/AVX-2 instruction sets. It is available for download here under the Affero GPL 3 License.

The corresponding documentation can be found here https://github.com/xflouris/libpll/wiki and a large porton of its functionality is presented the following examples.

MPTP: faster and more accurate species delimitation code

This tool is a significant improvement of our previous PTP tool for single-locus species delimitation. It is significantlky faster, more accurate, and more scalable with respect to the number of taxa.

The methods are described in this preprint, the code can be downloaded here, and there also is a web-service.

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. Xin Zhou, Paul B. Frandsen, Ralph W. Holzenthal, Clare R. Beet, Kristi R. Bennett, Roger J. Blahnik, Núria Bonada, David Cartwright, Suvdtsetseg Chuluunbat, Graeme V. Cocks, Gemma E. Collins, Jeremy deWaard, John Dean, Oliver S. Flint, Axel Hausmann, Lars Hendrich, Monika Hess, Ian D. Hogg, Boris C. Kondratieff, Hans Malicky, Megan A. Milton, Jérôme Morinière, John C. Morse, François Ngera Mwangi, Steffen U. Pauls, María Razo Gonzalez, Aki Rinne, Jason L. Robinson, Juha Salokannel, Michael Shackleton, Brian Smith, Alexandros Stamatakis, Ros StClair, Jessica A. Thomas, Carmen Zamora-Muñoz, Tanja Ziesmann, Karl M. Kjer: "The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life". In Philosophical Transactions of the Royal Society of London B: Biological Sciences, 371(1702), 2016, open access.
  2. Paschalia Kapli, Sarah Lutteropp, Jiajie Zhang, Kassian Kobert, Pavlos Pavlidis, Alexandros Stamatakis, Tomas Flouri: "Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo", BioRxiv, 063875, 2016, open access.
  3. 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.
  4. 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. Also published in Nucleic Acids Research open access
  5. 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.
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