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.

2016 summer school on computational molecular evolution

Applications will open in fall 2015 for the 8th summer school on computational molecular evolution organized by Nick Goldman, Aidan Budd, Ziheng Yang, Laura Emery and Alexis Stamatakis. It will be held once again in Crete.

To be notified once the web-site is up you can register at this link

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.

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. K. Kobert, L. Salichos, A. Rokas, A. Stamatakis: "Computing the Internode Certainty and related measures from partial gene trees." BioRxiv, 022053, 2015 open access.
  2. T. Flouri, E. Giaquinta, K. Kobert, E. Ukkonen: "Longest common substrings with k mismatches". In Information Processing Letters 115:643-647, 2015, open access.
  3. C. Barton, T. Flouri, C. S. Iliopoulos, S. P. Pissis: "Global and local sequence alignment with a bounded number of gaps". In Theoretical Computer Science, 2015, open access.
  4. A. M. Kozlov, A. J. Aberer, A. Stamatakis: "ExaML Version 3: A Tool for Phylogenomic Analyses on Supercomputers." In Bioinformatics, 2015 advance on-line access
  5. 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.

All publications >>