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

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.

Low Level Phylogenetic Likelihood Library version 2

This is version 2 of our low level phylogenetic likelihood library.

It now includes site repeats (see paper) to boost computations likelihood computations. It can be downloaded here and has been already integrated into RAxML-NG and Modeltest-NG (see below).

Completely re-designed Modeltest Software

We have completeley re-designed the famous Modeltest software. It's much faster, better, and more stable now.

The all new Modeltest can be downloaded here.

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.

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. Ralph S. Peters, Oliver Niehuis, Simon Gunkeld, Marcel Bläsere, Christoph Mayer, Lars Podsiadlowski, Alexey Kozlov, Alexander Donath,. Simon van Noort, Shanlin Liu, Xin Zhou. "Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success" In Molecular Phylogenetics and Evolution, 2018, advanced on-line access
  2. Rudolf Biczok, Peter Bozsoky, Peter Eisenmann, Johannes Ernst, Tobias Ribizel, Fedor Scholz, Axel Trefzer, Florian Weber, Michael Hamann, Alexandros Stamatakis. "Two C++ Libraries for Counting Trees on a Phylogenetic Terrace", BioRxiv, 211276, 2017 open access.
  3. Sarah Bank, Manuela Sann, Christoph Mayer, Karen Meusemann, Alexander Donath, Lars Podsiadlowski, Alexey Kozlov, Malte Petersen, Lars Krogmann, Rudolf Meier, Paolo Rosa, Thomas Schmitt, Mareike Wurdack, Shanlin Liu, Xin Zhou, Bernhard Misof, Ralph S Peters, Oliver Niehuis. "Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae)". In Molecular Phylogenetics and Evolution, 2017, advanced on-line access
  4. 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.
  5. 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.
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