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.

2015 summer school on computational molecular evolution

Applications are now open for the 7th summer school on computational molecular evolution organized by Nick Goldman, Aidan Budd, Ziheng Yang, Laura Emery and Alexis Stamatakis. The application deadline is November 14.

For further info and to apply on-line please visit the course page.

New Software

ExaBayes: Large Scale and Massively Parallel Bayesian Phylogenetic Inference

ExaBayes: A fast and scalable Bayesian inference tool for normal computers and supercomputers.

It is as fast or faster (on DNA data) than MrBayes and we demonstrated parallel scalability of up to 32,000 cores for it on the Munich supercomputing system: SuperMUC.

For more details, please visit the ExaBayes 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 8.0.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. E.D. Jarvis, S. Mirarab, A.J. Aberer, B. Li, P. Houde, C. Li, S.Y.W. Ho, B.C. Faircloth, B. Nabholz, J.T. Howard, A. Suh, C.C. Weber, R.R. da Fonseca, J. Li, F. Zhang, H. Li, L. Zhou, N. Narula, L. Liu, G. Ganapathy, B. Boussau, Md.S. Bayzid, V. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutiérrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W.C. Warren, D. Ray, R.E. Green, M.W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E.P. Derryberry, M. Frost Bertelsen, F.H. Sheldon, R.T. Brumfield, C.V. Mello, P.V. Lovell, M. Wirthlin, M. Paula Cruz Schneider, F. Prosdocimi, J. Alfredo Samaniego, A. Missael Vargas Velazquez, A. Alfaro-Nunez, P.F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D.M. Lambert, Q. Zhou, P. Perelman, A.C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F.E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F. Keith Barker, K. Andreas Jonsson, W. Johnson, K.-P. Koepfli, S. O’Brien, D. Haussler, O.A. Ryder, C. Rahbek, E. Willerslev, G.R. Graves, T.C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alström, S.V. Edwards, A. Stamatakis, D.P. Mindell, J. Cracraft, E.L. Braun, T. Warnow, W. Jun, M. Thomas P. Gilbert, G. Zhang: "Whole-genome analyses resolve early branches in the tree of life of modern birds". In Science, 46(6215):1320-1331, 2014. link to paper

    Our contribution:

    Alexis developed the initial version of the ExaML software for phylogenetic inference on supercomputers and applied for the computing time on the SuperMUC HPC system. Andre carried out the partitioning, phylogenetic analyses and some post-analyses on the SuperMUC using ExaML.

  2. G. Grimm, P. Kapli, B. Bomfleur, S. McLoughlin, S.S. Renner: "Using more than the oldest fossils: Dating Osmundaceae by three Bayesian clock approaches." In Systematic Biology, 2014, on-line access.
  3. B. Misof, S. Liu, K. Meusemann, R.S. Peters, A. Donath, C. Mayer, P.B. Frandsen, J. Ware, T. Flouri, R.G. Beutel, O. Niehuis, M. Petersen, F. Izquierdo-Carrasco, T. Wappler, J. Rust, A.J. Aberer, U. Aspöck, H. Aspöck, D. Bartel, A. Blanke, S. Berger, A. Böhm, T.R. Buckley, B. Calcott, J. Chen, F. Friedrich, M. Fukui, M. Fujita, C. Greve, P. Grobe, S. Gu, Y. Huang, L.S. Jermiin, A.Y. Kawahara, L. Krogmann, M. Kubiak, R. Lanfear, H. Letsch, Y. Li, Z. Li, J. Li, H. Lu, R. Machida, Y. Mashimo, P. Kapli, D.D. McKenna, G. Meng, Y. Nakagaki, J.L. Navarrete-Heredia, M. Ott, Y. Ou, G. Pass, L. Podsiadlowski, H. Pohl, B.M. von Reumont, K. Schütte, K. Sekiya, S. Shimizu, A. Slipinski, A. Stamatakis, W. Song, X. Su, N.U. Szucsich, M. Tan, X. Tan, M. Tang, J. Tang, G. Timelthaler, S. Tomizuka, M. Trautwein, X. Tong, T. Uchifune, M.G. Walzl, B.M. Wiegmann, J. Wilbrandt, B. Wipfler, T.K.F. Wong, Q. Wu, G. Wu, Y. Xie, S. Yang, Q. Yang, D.K. Yeates, K. Yoshizawa, Q. Zhang, R. Zhang, W. Zhang, Y. Zhang, J. Zhao, C. Zhou, L. Zhou, T. Ziesmann, S. Zou, Y. Li, X. Xu, Y. Zhang, H. Yang, J. Wang, J. Wang, K.M. Kjer, X. Zhou: "Phylogenomics resolves the timing and pattern of insect evolution". In Science, 346(6210): 763-767, 2014. link to paper

    English outreach video

    German outreach video

    Our contribution:

    Andre developped software for rogue taxon analysis and applied it to the datasets. Alexis developed the initial version of the ExaML software for phylogenetic inference on supercomputers and applied for the computing time on the SuperMUC HPC system. Simon and Fernando carried out the phylogenetic analyses on the SuperMUC using ExaML. Tomas and Paschalia substantially contributed to the dating analyses.

  4. T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L.-T. Nguyen, B.Q. Minh, A. von Haeseler, A. Stamatakis: "The Phylogenetic Likelihood Library". In Systematic Biology, 2014, open access.
  5. M.J. Sanderson, M.M. McMahon, A. Stamatakis, D.J. Zwickl, M. Steel: "Impacts of terraces on phylogenetic inference", Arxiv preprint, 2014, preprint.
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