CME Gruppe
Computational Molecular Evolution



  • David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P.F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth (2020). Eleven grand challenges in single-cell data science, Genome Biol 21(1) 1093
  • Ben Bettisworth, Alexandros Stamatakis (2020). RootDigger : a root placement program for phylogenetic trees, biorxiv;2020.02.13.935304v2,[Preprint] 1094



  • Diego Darriba, Tomáš Flouri, Alexandros Stamatakis (2018). The state of software for evolutionary biology, Molecular Biology and Evolution, 35(5):1037–1046 322
  • Diep Thi Hoang, Le Sy Vinh, Tomáš Flouri, Alexandros Stamatakis, Arndt von Häseler, Bui Quang Minh (2018). MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation, BMC Evolutionary Biology, 18(1):11 323
  • Nikolaos Psonis, Aglaia Antoniou, Emmanouela Karameta, Adam D Leaché, Panayiota Kotsakiozi, Diego Darriba, Alexey Kozlov, Alexandros Stamatakis, Dimitris Poursanidis, Oleg Kukushkin, others (2018). Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system, Molecular Phylogenetics and Evolution, 125:100–115 324
  • Pierre Barbera, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences, Systematic Biology 68(2):365-369 325
  • Kevin P Johnson, Christopher H Dietrich, Frank Friedrich, Rolf G Beutel, Benjamin Wipfler, Ralph S Peters, Julie M Allen, Malte Petersen, Alexander Donath, Kimberly KO Walden, others (2018). Phylogenomics and the evolution of hemipteroid insects, Proceedings of the National Academy of Sciences, pp. advance online access 326
  • Wolf L Eiserhardt, Alexandre Antonelli, Dominic J Bennett, Laura R Botigué, J Gordon Burleigh, Steven Dodsworth, Brian J Enquist, Félix Forest, Jan T Kim, Alexey M Kozlov, others (2018). A roadmap for global synthesis of the plant tree of life, American Journal of Botany, 105(3):614–622 327
  • David Bass, Lucas Czech, Bryony AP Williams, Cédric Berney, Micah Dunthorn, Frederic Mahé, Guifré Torruella, Grant D Stentiford, Tom A Williams (2018). Clarifying the Relationships between Microsporidia and Cryptomycota, Journal of Eukaryotic Microbiology, pp. 773-782 328
  • Thomas Pauli, Trevor O Burt, Karen Meusemann, Keith Bayless, Alexander Donath, Lars Podsiadlowski, Christoph Mayer, Alexey Kozlov, Alexandros Vasilikopoulos, Shanlin Liu, others (2018). New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae), Systematic Entomology, 43(3):447–459 329
  • Manuela Sann, Oliver Niehuis, Ralph S Peters, Christoph Mayer, Alexey Kozlov, Lars Podsiadlowski, Sarah Bank, Karen Meusemann, Bernhard Misof, Christoph Bleidorn, others (2018). Phylogenomic analysis of Apoidea sheds new light on the sister group of bees, BMC Evolutionary Biology, vol. 18(1), p. 71 330
  • Ralph S Peters, Oliver Niehuis, Simon Gunkel, Marcel Bläser, Christoph Mayer, Lars Podsiadlowski, Alexey Kozlov, Alexander Donath, Simon van Noort, Shanlin Liu, others (2018). Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success, Molecular Phylogenetics and Evolution, 120:286–296 331
  • Lucas Czech, Alexandros Stamatakis (2018). Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement, Bioinformatics, pp. advance online access 332
  • Lucas Czech, Alexandros Stamatakis (2018). Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements, bioRxiv, p. 346353 333
  • Benoit Morel, Alexey M Kozlov, Alexandros Stamatakis (2018). ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes., Bioinformatics 35(10):1771-1773 334
  • Alexandros Stamatakis (2018). Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges, In Population Genomics, Springer 335
  • Axel Trefzer, Alexandros Stamatakis (2018). Compressing Streams of Phylogenetic Trees, bioRxiv, p. 440644 336
  • Alexey Kozlov, Diego Darriba, Tomas Flouri, Benoit Morel, Alexandros Stamatakis (2018). RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference, bioRxiv, p. 447110 337


  • Benoit Morel, Tomas Flouri, Alexandros Stamatakis (2017). A novel heuristic for data distribution in massively parallel phylogenetic inference using site repeats, In Proceedings of 19th Conference on High Performance Computing and Communications (HPCC), Bangkok, Thailand., IEEE, Dec 2017 217
  • Lucas Czech, Jaime Huerta-Cepas, Alexandros Stamatakis (2017). A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits, Molecular Biology and Evolution 34(6):1535-1542 113
  • Cédric Berney, Andreea Ciuprina, Sara Bender, Juliet Brodie, Virginia Edgcomb, Eunsoo Kim, Jeena Rajan, Laura Wegener Parfrey, Sina Adl, Stéphane Audic, others (2017). UniEuk: Time to Speak a Common Language in Protistology!, Journal of Eukaryotic Microbiology, 64(3):407-411 212
  • Oliver Ratmann, Chris Wymant, Caroline Colijn, Siva Danaviah, M Essex, Simon DW Frost, Astrid Gall, Simani Gaiseitsiwe, Mary Grabowski, Ronald Gray, others (2017). HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences, AIDS Research and Human Retroviruses, 33(11):1083-1098 213
  • Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz von Looz, Antonis Rokas (2017). Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence, biorxiv;168526v1,[Preprint] 214
  • Tomas Flouri, Jiajie Zhang, Lucas Czech, Kassian Kobert, Alexandros Stamatakis (2017). An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties, In Algorithms for Next-Generation Sequencing Data, pp. 299-325, Springer 215
  • R. Biczok, P. Bozsoky, P. Eisenmann, J. Ernst, T. Ribizel, F. Scholz, A. Trefzer, F. Weber, M. Hamann, A. Stamatakis (2017). Two C++ Libraries for Counting Trees on a Phylogenetic Terrace, biorxiv;211276v1,[Preprint] 216
  • Sarah Bank, Manuela Sann, Christoph Mayer, Karen Meusemann, Alexander Donath, Lars Podsiadlowski, Alexey Kozlov, Malte Petersen, Lars Krogmann, Rudolf Meier, others (2017). Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae), Molecular Phylogenetics and Evolution, 116:213-226 218
  • Ralph S Peters, Lars Krogmann, Christoph Mayer, Alexander Donath, Simon Gunkel, Karen Meusemann, Alexey Kozlov, Lars Podsiadlowski, Malte Petersen, Robert Lanfear, others (2017). Evolutionary history of the Hymenoptera, Current Biology, 27(7):1013-1018 219
  • J Šmíd, J Moravec, V Gvoždík, J Štundl, D Frynta, P Lymberakis, P Kapli, T Wilms, A Schmitz, M Shobrak, SH Yousefkhani, E Rastegar-Pouyani, AM Castilla, J Els, W Mayer (2017). Cutting the Gordian Knot: Phylogenetic and ecological diversification of the Mesalina brevirostris species complex (Squamata, Lacertidae), Zoologica Scripta, 46(6):649-664 220
  • Faraham Ahmadzadeh, Petros Lymberakis, Reyhaneh Saberi Pirouz, Paschalia Kapli (2017). The evolutionary history of two lizards (Squamata: Lacertidae) is linked to the geological development of Iran, Zoologischer Anzeiger – A Journal of Comparative Zoology, 270(Supplement C):49-56 221
  • F Grímsson, P Kapli, C-C Hofmann, R Zetter, GW Grimm (2017). Eocene Loranthaceae pollen pushes back divergence ages for major splits in the family, PeerJ, 5:e3373 222


  • Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé (2016). VSEARCH: a versatile open source tool for metagenomics, PeerJ, 4:e2584, Oct 2016 123
  • Frédéric Mahé, Colomban de Vargas, David Bass, Lucas Czech, Alexandros Stamatakis, Enrique Lara, David Singer, Jordan Mayor, John Bunge, Sarah Sernaker, Tobias Siemensmeyer, Isabelle Trautmann, Sarah Romac, Cédric Berney, Alexey Kozlov, Edward A.D. Mitchell, Christophe V. W. Seppey, Elianne Egge, Guillaume Lentendu, Rainer Wirth, Gabriel Trueba, Micah Dunthorn (2016). Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites, biorxiv;050997v3,[Preprint] 114
  • Constantin Scholl, Kassian Kobert, Tomá Flouri, Alexandros Stamatakis (2016). The divisible load balance problem with shared cost and its application to phylogenetic inference, In Parallel and Distributed Processing Symposium Workshops, 2016 IEEE International, pp. 408–417 115
  • Diego Darriba, Michael Weiß, Alexandros Stamatakis (2016). Prediction of missing sequences and branch lengths in phylogenomic data, Bioinformatics, 32(9):1331–1337 116
  • Michael Hoff, Stefan Orf, Benedikt Riehm, Diego Darriba, Alexandros Stamatakis (2016). Does the choice of nucleotide substitution models matter topologically?, BMC Bioinformatics, 17(1):143 117
  • Eirini Skourtanioti, Paschalia Kapli, Çetin Ilgaz, Yusuf Kumlutaş, Aziz Avcı, Faraham Ahmadzadeh, Jelka Crnobrnja–Isailović, Iulian Gherghel, Petros Lymberakis, Nikos Poulakakis (2016). A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes, Molecular Phylogenetics and Evolution, 103:199–214 118
  • Faraham Ahmadzadeh, Morris Flecks, Miguel A. Carretero, Wolfgang Böhme, Flora Ihlow, Paschalia Kapli, Andreia Miraldo, Dennis Rödder (2016). Separate histories in both sides of the Mediterranean: phylogeny and niche evolution of ocellated lizards, Journal of Biogeography, 43(6):1242–1253 119
  • Panagiotis Kornilios, Evanthia Thanou, Paschalia Kapli, Aristidis Parmakelis, Maria Chatzaki (2016). Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae, Molecular Phylogenetics and Evolution, 98:300–313 120
  • Susanne S Renner, Guido W Grimm, Paschalia Kapli, Thomas Denk (2016). Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth–death clock model, Phil. Trans. R. Soc. B, 371(1699):20150135 121
  • Kassian Kobert, Alexandros Stamatakis, Tomáš Flouri (2016). Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations, Systematic Biology 122
  • Alexey M Kozlov, Jiajie Zhang, Pelin Yilmaz, Frank Oliver Glöckner, Alexandros Stamatakis (2016). Phylogeny-aware identification and correction of taxonomically mislabeled sequences, Nucleic Acids Research, 44(11):5022–5033 124
  • P. Kapli, S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis, T. Flouri (2016). Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo, biorxiv;063875v1,[Preprint] 125
  • 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, others (2016). The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life, Phil. Trans. R. Soc. B, vol. 371(1702), p. 20160025 126
  • Diep Thi Hoang, Le Sy Vinh, Tomas Flouri, Alexandros Stamatakis, Arndt von Häseler, Bui Quang Minh (2016). A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation, In Knowledge and Systems Engineering (KSE), 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE), Hanoi, 2016, pp. 1–6 127




  • Alexey Kozlov (2018). Models, Optimizations, and Tools for Large-Scale Phylogenetic Inference, Handling Sequence Uncertainty, and Taxonomic Validation, Computer Science, Karlsruhe Institute of Technology, 2018, Alexandros Stamatakis(HITS Tutor) 321


  • Diego Darriba (2016). Selection of models of genomic evolution in HPC environments, Computer Science, University of A Coruna, 2016, Guillermo López Taboada(Tutor), Alexandros Stamatakis(HITS Tutor) 110
  • Kassian Kobert (2016). Mathematical Problems in Molecular Evolution and Next Generation Sequencing, Computer Science, Karlsruhe Institute of Technology, 2016, Alexandros Stamatakis(Tutor) 111
  • Nikolaos Psonis (2016). Molecular Phylogeny and Phylogeography of the Podarcis tauricus (Sauria: Lacertidae) Species Subgroup, Department of Biology, University of Crete, 2016, Nikolaos Poulakakis(Tutor), Alexandros Stamatakis(HITS Tutor) 112

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