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.

2018 summer school on computational molecular evolution

Applications are now open for the 10th summer school on computational molecular evolution organized by Nick Goldman, Ziheng Yang, Cilia Antoniou, Laura Emery and Alexis Stamatakis. It will be held once again in Heraklion, Crete, Greece.

See the course page for further details

New Software

RAxML next generation

The new, from scratch re-implementation of RAxML is finally avaible at github.

It's faster, more stable, easier to use, and more scalable

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. Benoit Morel, Tomas Flouri, Alexandros Stamatakis "A novel heuristic for data distribution in massively parallel phylogenetic inference using site repeats", accepted for publication at HPCC17.
  2. Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz von Looz, Antonis Rokas. "Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence", BioRxiv, 168526, 2017, open access.
  3. Oliver Ratmann, Chris Wymant, Caroline Colijn, Siva Danaviah, Max Essex, Simon Frost, Astrid Gall, Simani Gaseitsiwe, Mary Grabowski, Ronald Gray, Stephane Guindon, Arndt von Haeseler, Pontiano Kaleebu, Michelle Kendall, Alexey Kozlov, Justen Manasa, Bui Quang Minh, Sikhulile Moyo, Vlad Novitsky, Rebecca Nsubuga, Sureshnee Pillay, Thomas C. Quinn, David Serwadda, Deogratius Ssemwanga, Alexandros Stamatakis, Jana Trifinopoulos, Maria Wawer, Andy Leigh Brown, Tulio de Oliveira, Paul Kellam, Deenan Pillay and Christophe Fraser on behalf of the PANGEA‐HIV Consortium. "HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences". In AIDS Research and Human Retroviruses, 2017, advance on-line access.
  4. Ralph S Peters, Lars Krogmann, Christoph Mayer, Alexander Donath, Simon Gunkel, Karen Meusemann, Alexey Kozlov, Lars Podsiadlowski, Malte Petersen, Robert Lanfear, Patricia A Diez, John Heraty, Karl M Kjer, Seraina Klopfstein, Rudolf Meier, Carlo Polidori, Thomas Schmitt, Shanlin Liu, Xin Zhou, Torsten Wappler, Jes Rust, Bernhard Misof, Oliver Niehuis "Evolutionary history of the Hymenoptera". In Current Biology, 2017, on-line access.
  5. Cédric Berney, Andreea Ciuprina, Sara Bender, Juliet Brodie, Virginia Edgcomb, Eunsoo Kim, Jeena Rajan, Laura Wegener Parfrey, Sina Adl, Stéphane Audic, David Bass, David A Caron, Guy Cochrane, Lucas Czech, Micah Dunthorn, Stefan Geisen, Frank Oliver Glöckner, Frédéric Mahé, Christian Quast, Jonathan Z Kaye, Alastair GB Simpson, Alexandros Stamatakis, Javier del Campo, Pelin Yilmaz, Colomban Vargas: "UniEuk: Time to Speak a Common Language in Protistology!". In Journal of Eukaryotic Microbiology, 2017, on-line access.
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