Prof. Dr. Alexandros Stamatakis

2023

• Morel B, Williams TA, Stamatakis A, Szöllősi GJ (2023). AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss, biorxiv;2023.10.06.561091v2,[Preprint] 1751
• Togkousidis A, Kozlov OM, Haag J, Höhler D, Stamatakis A (2023). Adaptive RAxML-NG: Accelerating Phylogenetic Inference under Maximum Likelihood using Dataset Difficulty, Molecular Biology and Evolution 40(10),msad227 1750
• Ewers I, Rajter L, Czech L, Mahé F, Stamatakis A, Dunthorn M (2023). Interpreting phylogenetic placements for taxonomic assignment of environmental DNA, J Eukaryotic Microbiology 70(5),e12990 1748
• Trost J, Haag J, Höhler D, Jacob L, Stamatakis A, Boussau B (2023). Simulations of sequence evolution: how (un)realistic they are and why, biorxiv;2023.07.11.548509v2,[Preprint] 1747
• Togkousidis A, Chernomor O, Stamatakis A (2023). Parallel Inference of Phylogenetic Stands with Gentrius, 2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW),pp.139-148,IEEE 1746
• Williams TA, Davin AA, Morel B, Szánthó LL, Spang A, Stamatakis A, Hugenholtz P, Szöllősi GJ (2023). The power and limitations of species tree-aware phylogenetics, biorxiv;2023.03.17.533068v1,[Preprint] 1745
• Koptekin D, Yüncü E, Rodríguez-Varela R, Altınışık NE, Psonis N, Kashuba N, Yorulmaz S, George R, Kazancı DD, Kaptan D, Gürün K, Vural KB, Gemici HC, Vassou D, Daskalaki E, Karamurat C, Lagerholm VK, Erdal ÖD, Kırdök E, Marangoni A, Schachner A, Üstündağ H, Shengelia R, Bitadze L, Elashvili M, Stravopodi E, Özbaşaran M, Duru G, Nafplioti A, Rose CB, Gencer T, Darbyshire G, Gavashelishvili A, Pitskhelauri K, Çevik Ö, Vuruşkan O, Kyparissi-Apostolika N, Büyükkarakaya AM, Oğuzhanoğlu U, Günel S, Tabakaki E, Aliev A, Ibrahimov A, Shadlinski V, Sampson A, Kılınç GM, Atakuman Ç, Stamatakis A, Poulakakis N, Erdal YS, Pavlidis P, Storå J, Özer F, Götherström A, Somel M (2023). Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean, Current Biology 33(1):41-57.e15 1742
• Morel B, Williams TA, Stamatakis A (2023). Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data, Bioinformatics 39(1),btac832 1744
• Haag J, Hübner L, Kozlov AM, Stamatakis A (2023). The Free Lunch is not over yet—systematic exploration of numerical thresholds in maximum likelihood phylogenetic inference, Bioinformatics Advances 3(1),vbad124 1749
• Psonis N, Vassou D, Nafplioti A, Tabakaki E, Pavlidis P, Stamatakis A, Poulakakis N (2023). Identification of the 18 World War II Executed Citizens of Adele, Rethymnon, Crete Using an Ancient DNA Approach and Low Coverage Genomes, [Preprint] 1752

2022

• Haag J, Höhler D, Bettisworth B, Stamatakis A (2022). From Easy to Hopeless—Predicting the Difficulty of Phylogenetic Analyses, Molecular Biology and Evolution 39(12),msac254 1740
• Höhler D, Haag J, Kozlov AM, Stamatakis A (2022). A representative Performance Assessment of Maximum Likelihood based Phylogenetic Inference Tools, biorxiv;2022.10.31.514545v1,[Preprint] 1741
• Hubner L, Hespe D, Sanders P, Stamatakis A (2022). ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms, 2022 IEEE/ACM 12th Workshop on Fault Tolerance for HPC at eXtreme Scale (FTXS),pp.24-35,IEEE 1743
• Haag J, Hübner L, Kozlov AM, Stamatakis A (2022). The Free Lunch is not over yet – Systematic Exploration of Numerical Thresholds in Phylogenetic Inference, biorxiv;2022.07.13.499893v1,[Preprint] 1537
• Haag J, Höhler D, Bettisworth B, Stamatakis A (2022). From Easy to Hopeless – Predicting the Difficulty of Phylogenetic Analyses, biorxiv;2022.06.20.496790v1,[Preprint] 1536
• Czech L, Stamatakis A, Dunthorn M, Barbera P (2022). Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade, Front. Bioinform. 2,871393 1534
• Bettisworth B, Smith SA, Stamatakis A (2022). Lagrange-NG: The next generation of Lagrange, biorxiv;2022.04.19.488734v1,[Preprint] 1535
• Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N (2022). SPART: A versatile and standardized data exchange format for species partition information, Molecular Ecology Resources 22(1):430-438 1430

2021

• Höhler D, Pfeiffer W, Ioannidis V, Stockinger H, Stamatakis A (2021). RAxML Grove: An empirical Phylogenetic Tree Database, biorxiv;2021.10.05.463179v2,[Preprint] 1431
• Lutteropp S, Scornavacca C, Kozlov AM, Morel B, Stamatakis A (2021). NetRAX: Accurate and Fast Maximum Likelihood Phylogenetic Network Inference ⋆, biorxiv;2021.08.30.458194v1,[Preprint] 1296
• Mahé F, Czech L, Stamatakis A, Quince C, Vargas Cd, Dunthorn M, Rognes T (2021). Swarm v3: towards tera-scale amplicon clustering, Bioinformatics,btab493 1297
• Bettisworth B, Stamatakis A (2021). Phylourny: Predicting the Knock-out-phase of Tournaments via Phylogenetic Methods by example of the UEFA EURO 2020, biorxiv;2021.06.24.449715v1,[Preprint] 1279
• Psonis N, Antoniou A, Karameta E, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N (2021). The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics, Molecular Phylogenetics and Evolution 159:107121 1300
• Morel B, Schade P, Lutteropp S, Williams TA, Szöllősi GJ, Stamatakis A (2021). SpeciesRax: A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss, biorxiv;2021.03.29.437460v1,[Preprint] 1298
• Miralles A, Ducasse J, Brouillet S, Flouri T, Fujisawa T, Kapli P, Knowles LL, Kumari S, Stamatakis A, Sukumaran J, Lutteropp S, Vences M, Puillandre N (2021). SPART, a versatile and standardized data exchange format for species partition information, biorxiv;2021.03.22.435428v1,[Preprint] 1299
• Hodcroft EB, Maio ND, Lanfear R, MacCannell DR, Minh BQ, Schmidt HA, Stamatakis A, Goldman N, Dessimoz C (2021). Want to track pandemic variants faster? Fix the bioinformatics bottleneck, Nature 591(7848):30-33 1302

2020

• Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki E, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A (2020). Phylogenetic analysis of SARS-CoV-2 data is difficult, Molecular Biology and Evolution,msaa314 1157
• Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson Bd, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder Jd, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A (2020). Eleven grand challenges in single-cell data science, Genome Biol 21(1) 1093
• Gornik SG, Bergheim BG, Morel B, Stamatakis A, Foulkes NS, Guse A (2020). Photoreceptor diversification accompanies the evolution of Anthozoa, Molecular Biology and Evolution,msaa304 1158
• Zapletal A, Höhler D, Sinz C, Stamatakis A (2020). SoftWipe – a tool and benchmark to assess scientific software quality, biorxiv;2020.10.07.330621v2,[Preprint] 1153
• Barbera P, Czech L, Lutteropp S, Stamatakis A (2020). SCRAPP : A tool to assess the diversity of microbial samples from phylogenetic placements, Mol Ecol Resour,1755-0998.13255 1149
• Kozlov A, Alves J, Stamatakis A, Posada D (2020). CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data, biorxiv;2020.07.31.230292v1,[Preprint] 1150
• Lutteropp S, Kozlov AM, Stamatakis A (2020). A fast and memory-efficient implementation of the transfer bootstrap, Bioinformatics 36(7):2280-2281 1160
• Bettisworth B, Stamatakis A (2020). RootDigger : a root placement program for phylogenetic trees, biorxiv;2020.02.13.935304v2,[Preprint] 1094

2019

• Breitling P, Stamatakis A, Chernomor O, Bettisworth B, Reszczynski L (2019). Empirical Analysis of Phylogenetic Quasi-Terraces, biorxiv;810309v1,[Preprint] 476
• Comte N, Morel B, Hasic D, Guéguen L, Boussau B, Daubin V, Penel S, Scornavacca C, Gouy M, Stamatakis A, Tannier E, Parsons DP (2019). Treerecs: an integrated phylogenetic tool, from sequences to reconciliations, biorxiv;782946v1,[Preprint] 477
• Morel B, Kozlov AM, Stamatakis A, Szöllősi GJ (2019). GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss, biorxiv;779066v1,[Preprint] 483
• Perron U, Kozlov AM, Stamatakis A, Goldman N, Moal IH (2019). Modeling Structural Constraints on Protein Evolution via Side-Chain Conformational States, Molecular Biology and Evolution 36(9):2086-2103 484
• Zhou X, Lutteropp S, Czech L, Stamatakis A, Looz MV, Rokas A (2019). Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence, Systematic Biology 69(2):308–324 904
• Laehnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Beerenwinkel N, Campbell KR, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson Bd, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kiełbasa SM, Korbel JO, Kozlov AM, Kuo T, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowski Ł, Reinders M, Ridder Jd, Saliba A, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A (2019). 12 Grand Challenges in Single-Cell Data Science, e27885v3,[Preprint] 481
• Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T (2019). ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models, Molecular Biology and Evolution 37(1):291-294 478
• Czech L, Barbera P, Stamatakis A (2019). Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data, biorxiv;647958v3,[Preprint] 480
• Kozlov AM, Stamatakis A (2019). Using RAxML-NG in Practice, [Preprint] 951
• Jamy M, Foster R, Barbera P, Czech L, Kozlov A, Stamatakis A, Baß D, Burki F (2019). Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity, Mol Ecol Resour.00:1-15 479
• Baar I, Hubner L, Oettig P, Zapletal A, Schlag S, Stamatakis A, Morel B (2019). Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning, 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW),pp.175-184,IEEE 741
• Stamatakis A (2019). A review of approaches for optimizing phylogenetic likelihood calculations, In Bioinformatics and Phylogenetics, pp. 1–19, Springer 902
• Serdari D, Kostaki E, Paraskevis D, Stamatakis A, Kapli P (2019). Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV, PeerJ 7:e7754 905

2018

• Darriba D, Flouri T, Stamatakis A (2018). The state of software for evolutionary biology, Molecular Biology and Evolution, 35(5):1037–1046 322
• Hoang DT, Vinh LS, Flouri T, Stamatakis A, Häseler Av, Minh BQ (2018). MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation, BMC Evolutionary Biology, 18(1):11 323
• Psonis N, Antoniou A, Karameta E, Leaché AD, Kotsakiozi P, Darriba D, Kozlov A, Stamatakis A, Poursanidis D, Kukushkin O, 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
• Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A (2018). EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences, Systematic Biology 68(2):365-369 325
• Czech L, Stamatakis A (2018). Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement, Bioinformatics, pp. advance online access 332
• Czech L, Stamatakis A (2018). Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements, bioRxiv, p. 346353 333
• Morel B, Kozlov AM, Stamatakis A (2018). ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes., Bioinformatics 35(10):1771-1773 334
• Stamatakis A (2018). Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges, In Population Genomics, Springer 335
• Trefzer A, Stamatakis A (2018). Compressing Streams of Phylogenetic Trees, bioRxiv, p. 440644 336
• Kozlov A, Darriba D, Flouri T, Morel B, Stamatakis A (2018). RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference, bioRxiv, p. 447110 337

2017

• Morel B, Flouri T, Stamatakis A (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
• Czech L, Huerta-Cepas J, Stamatakis A (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
• Zhou X, Lutteropp S, Czech L, Stamatakis A, Looz Mv, Rokas A (2017). Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence, biorxiv;168526v1,[Preprint] 214
• Flouri T, Zhang J, Czech L, Kobert K, Stamatakis A (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
• Biczok R, Bozsoky P, Eisenmann P, Ernst J, Ribizel T, Scholz F, Trefzer A, Weber F, Hamann M, Stamatakis A (2017). Two C++ Libraries for Counting Trees on a Phylogenetic Terrace, biorxiv;211276v1,[Preprint] 216

2016

• Mahé F, Vargas Cd, Bass D, Czech L, Stamatakis A, Lara E, Singer D, Mayor J, Bunge J, Sernaker S, Siemensmeyer T, Trautmann I, Romac S, Berney C, Kozlov A, Mitchell EA, Seppey CVW, Egge E, Lentendu G, Wirth R, Trueba G, Dunthorn M (2016). Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites, biorxiv;050997v3,[Preprint] 114
• Scholl C, Kobert K, Flouri T, Stamatakis A (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
• Darriba D, Weiß M, Stamatakis A (2016). Prediction of missing sequences and branch lengths in phylogenomic data, Bioinformatics, 32(9):1331–1337 116
• Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A (2016). Does the choice of nucleotide substitution models matter topologically?, BMC Bioinformatics, 17(1):143 117
• Kobert K, Stamatakis A, Flouri T (2016). Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations, Systematic Biology 122
• Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A (2016). Phylogeny-aware identification and correction of taxonomically mislabeled sequences, Nucleic Acids Research, 44(11):5022–5033 124
• Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T (2016). Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo, biorxiv;063875v1,[Preprint] 125
• Hoang DT, Vinh LS, Flouri T, Stamatakis A, Häseler Av, Minh BQ (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

2015

• Aberer AJ, Stamatakis A, Ronquist F (2015). An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees, Syst Biol 65(1):161-176 77
• Leaché AD, Banbury BL, Felsenstein J, Oca And, Stamatakis A (2015). Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies, Syst Biol 64(6):1032-1047 76
• Sanderson MJ, McMahon MM, Stamatakis A, Zwickl DJ, Steel M (2015). Impacts of Terraces on Phylogenetic Inference, Syst Biol 64(5):709-726 72
• Kozlov AM, Aberer AJ, Stamatakis A (2015). ExaML version 3: a tool for phylogenomic analyses on supercomputers, Bioinformatics 31(15):2577-2579 74
• Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer A, Nguyen L, Minh B, Häseler AV, Stamatakis A (2015). The phylogenetic likelihood library, Systematic Biology, 64(2):356–362 71
• Kobert K, Salichos L, Rokas A, Stamatakis A (2015). Computing the Internode Certainty and related measures from partial gene trees., biorxiv;022053v2,[Preprint] 75
• Stamatakis A (2015). Using RAxML to Infer Phylogenies, Current Protocols in Bioinformatics, pp. 6–14 78
• Flouri T, Kobert K, Rognes T, Stamatakis A (2015). Are all global alignment algorithms and implementations correct?, biorxiv;031500v1,[Preprint] 79
• Darriba D, Flouri T, Stamatakis A (2015). The State of Software in Evolutionary Biology, biorxiv;031930v1,[Preprint] 80
• Baudis N, Barbera P, Graf S, Lutteropp S, Opitz D, Flouri T, Stamatakis A (2015). Two Independent and Highly Efficient Open Source TKF91 Implementations, biorxiv;033191v1,[Preprint] 81
• Czech L, Stamatakis A (2015). Do Phylogenetic Tree Viewers correctly display Support Values?, biorxiv;035360v4,[Preprint] 82

2013

• Fuller JC, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos TG, Linssen K, Rajput AM (2013). Biggest challenges in bioinformatics, EMBO Rep 14(4):302-304 739