Alexandros Stamatakis

Jiajie Zhang, Alexandros Stamatakis, A. Stamatakis, 2012, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum.

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples

Alexandros Stamatakis, Lucas Czech, 2019 .

Phylogenetic Bootstrapping under Resource Constraints: Higher Model Accuracy or more Replicates?

Alexandros Stamatakis, Vincent Rousset, 2008 .

Phylogenetic models of rate heterogeneity: a high performance computing perspective

Alexandros Stamatakis, A. Stamatakis, 2006, Proceedings 20th IEEE International Parallel & Distributed Processing Symposium.

Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

Alexandros Stamatakis, Lucas Czech, Pierre Barbera, 2020, Bioinform..

Result verification, code verification and computation of support values in phylogenetics

Alexandros Stamatakis, Fernando Izquierdo-Carrasco, A. Stamatakis, 2011, Briefings Bioinform..

PUmPER: phylogenies updated perpetually

Alexandros Stamatakis, John Cazes, Fernando Izquierdo-Carrasco, 2014, Bioinform..

A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm

Alexandros Stamatakis, Nikolaos Alachiotis, 2011, Int. J. Reconfigurable Comput..

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Benoit Morel, Alexandros Stamatakis, Simon Penel, 2020, Bioinformatics.

ExaML version 3: a tool for phylogenomic analyses on supercomputers

Alexey M. Kozlov, Alexandros Stamatakis, Alexey M. Kozlov, 2015, Bioinform..

Trading Running Time for Memory in Phylogenetic Likelihood Computations

Alexandros Stamatakis, Julien Gagneur, Fernando Izquierdo-Carrasco, 2012, BIOINFORMATICS.

ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes

Alexey M. Kozlov, Alexandros Stamatakis, Benoit Morel, 2018, bioRxiv.

Parallel Computing in Phylogenetics

Aidan Budd, Alexandros Stamatakis, 2014 .

Are all global alignment algorithms and implementations correct?

Alexandros Stamatakis, Torbjørn Rognes, Kassian Kobert, 2015, bioRxiv.

Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell

Alexandros Stamatakis, Dimitrios S. Nikolopoulos, Christos D. Antonopoulos, 2007, J. VLSI Signal Process..

FPGA Optimizations for a Pipelined Floating-Point Exponential Unit

Alexandros Stamatakis, Nikolaos Alachiotis, 2011, ARC.

Rapid forward-in-time simulation at the chromosome and genome level

Alexandros Stamatakis, Andre J. Aberer, 2013, BMC Bioinformatics.

Computing the Phylogenetic Likelihood Function Out-of-Core

Alexandros Stamatakis, Fernando Izquierdo-Carrasco, A. Stamatakis, 2011, 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum.

DRAxML at home: a distributed program for computation of large phylogenetic trees

Thomas Ludwig, Alexandros Stamatakis, Michael Ott, 2005, Future Gener. Comput. Syst..

AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction

Alexandros Stamatakis, Simon A. Berger, 2009, PPAM.

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

Alexandros Stamatakis, Michael Ott, A. Stamatakis, 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

Parallel computation of phylogenetic consensus trees

Alexandros Stamatakis, Nicholas D. Pattengale, Andre J. Aberer, 2010, ICCS.

Phylogenetic Placement of Short Reads

Alexandros Stamatakis, Aidan Budd Erick Matsen, 2014 .

A reconfigurable architecture for the Phylogenetic Likelihood Function

Alexandros Stamatakis, Nikolaos S. Alachiotis, Apostolos Dollas, 2009, 2009 International Conference on Field Programmable Logic and Applications.

Using Treemaps to Visualize Phylogenetic Trees

Ioannis G. Tollis, Alexandros Stamatakis, Martin Reczko, 2005, ISBMDA.

Using RAxML-NG in Practice

Alexey M. Kozlov, Alexandros Stamatakis, Alexey M Kozlov, 2019 .

Evolutionary placement of short sequence reads on multi-core architectures

Alexandros Stamatakis, Simon A. Berger, Zsolt Komornik, 2010, ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010.

An Optimal Algorithm for Computing All Subtree Repeats in Trees

Solon P. Pissis, Alexandros Stamatakis, Kassian Kobert, 2013, IWOCA.

Orchestrating the Phylogenetic Likelihood Function on Emerging Parallel Architectures

Alexandros Stamatakis, 2010 .

Parallel Inference of a 10.000-Taxon Phylogeny with Maximum Likelihood

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2004, Euro-Par.

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis, A. Stamatakis, 2014, Bioinform..

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets

Alexandros Stamatakis, Pavlos Pavlidis, Nikolaos S. Alachiotis, 2012, Bioinform..

Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data

Alexandros Stamatakis, Nikolaos S. Alachiotis, Nikolaos Alachiotis, 2010, Bioinform..

ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection

Alexandros Stamatakis, Pavlos Pavlidis, Nikolaos S. Alachiotis, 2013, Computational and structural biotechnology journal.

Scalable Methods for Post-Processing, Visualizing, and Analyzing Phylogenetic Placements

Alexandros Stamatakis, Lucas Czech, A. Stamatakis, 2018, bioRxiv.

RAxML-Light: a tool for computing terabyte phylogenies

Alexandros Stamatakis, Fernando Izquierdo-Carrasco, Stephen A. Smith, 2012, Bioinform..

Large-scale phylogenetic analysis on current HPC architectures

Srinivas Aluru, Alexandros Stamatakis, Michael Ott, 2008, Sci. Program..

Parallel Ocean Program (POP)

Rudolf Eigenmann, Bernd Mohr, Stefan Schmid, 2011, Encyclopedia of Parallel Computing.

FPGA Acceleration of the Phylogenetic Parsimony Kernel?

Alexandros Stamatakis, Nikolaos S. Alachiotis, Nikolaos Alachiotis, 2011, 2011 21st International Conference on Field Programmable Logic and Applications.

Heuristic Algorithms for the Protein Model Assignment Problem

Michael Gertz, Alexandros Stamatakis, Bernhard Misof, 2013, ISBRA.

Compressing Streams of Phylogenetic Trees

Alexandros Stamatakis, Axel Trefzer, 2018 .

A fast program for maximum likelihood-based inference of large phylogenetic trees

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2004, SAC '04.

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

Jiajie Zhang, Alexandros Stamatakis, Tomás Flouri, 2013, Bioinform..

Exploring FPGAs for accelerating the phylogenetic likelihood function

Alexandros Stamatakis, Nikolaos S. Alachiotis, Apostolos Dollas, 2009, 2009 IEEE International Symposium on Parallel & Distributed Processing.

Accelerating String Matching on MIC Architecture for Motif Extraction

Solon P. Pissis, Alexandros Stamatakis, Pavlos Pavlidis, 2013, PPAM.

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

B. S. Manjunath, Ali Akoglu, Lars Koesterke, 2011, Front. Plant Sci..

Do Phylogenetic Tree Viewers correctly display Support Values

Alexandros Stamatakis, Lucas Czech, 2015 .

Dynamic multigrain parallelization on the cell broadband engine

Alexandros Stamatakis, Dimitrios S. Nikolopoulos, Christos D. Antonopoulos, 2007, PPoPP.

Particle Methods

Rudolf Eigenmann, Davide Sangiorgi, Paul Feautrier, 2011, Encyclopedia of Parallel Computing.

Distributed and parallel algorithms and systems for inference of huge phylogenetic trees based on the maximum likelihood method

Alexandros Stamatakis, A. Stamatakis, 2004 .

A Fast Program for Phylogenetic Tree Inference with Maximum Likelihood

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2005 .

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

Alexandros Stamatakis, A. Stamatakis, 2006, Bioinform..

An efficient program for phylogenetic inference using simulated annealing

Alexandros Stamatakis, A. Stamatakis, 2005, 19th IEEE International Parallel and Distributed Processing Symposium.

Libgapmis: An ultrafast library for short-read single-gap alignment

Solon P. Pissis, Alexandros Stamatakis, Tomás Flouri, 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops.

A generic and versatile architecture for inference of evolutionary trees under maximum likelihood

Alexandros Stamatakis, Nikolaos S. Alachiotis, Nikolaos Alachiotis, 2010, 2010 Conference Record of the Forty Fourth Asilomar Conference on Signals, Systems and Computers.

Tool environments in CORBA-based medical high-performance computing

Thomas Ludwig, Alexandros Stamatakis, Günther Rackl, 2002, Future Gener. Comput. Syst..

SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

Christoph Pacher, Alexandros Stamatakis, Ziheng Yang, 2012, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum.

How Many Bootstrap Replicates Are Necessary?

Alexandros Stamatakis, Bernard M. E. Moret, Nicholas D. Pattengale, 2009, RECOMB.

Methods for automatic reference trees and multilevel phylogenetic placement

Alexandros Stamatakis, Lucas Czech, Pierre Barbera, 2018, bioRxiv.

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data

Alexey M. Kozlov, Alexandros Stamatakis, David Posada, 2020, Genome Biology.

SoftWipe – a tool and benchmark to assess scientific software quality

Alexandros Stamatakis, Carsten Sinz, Adrian Zapletal, 2020 .

scrapp: A tool to assess the diversity of microbial samples from phylogenetic placements

Alexandros Stamatakis, Lucas Czech, Pierre Barbera, 2020, bioRxiv.

The AxML program family for maximum likelihood-based phylogenetic tree inference: Research Articles

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2004 .

Inference of Huge Trees under Maximum Likelihood

Alexandros Stamatakis, Fernando Izquierdo-Carrasco, 2012, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum.

Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs

Alexandros Stamatakis, Nikolaos S. Alachiotis, Nikolaos Alachiotis, 2011, 2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines.

Phylogenetic tree inference on PC architectures with AxML/PAxML

Thomas Ludwig, Alexandros Stamatakis, 2003, Proceedings International Parallel and Distributed Processing Symposium.

Efficient Computation of the Phylogenetic Likelihood Function on the Intel MIC Architecture

Alexey M. Kozlov, Alexandros Stamatakis, Alexey M. Kozlov, 2014, 2014 IEEE International Parallel & Distributed Processing Symposium Workshops.

Accuracy of morphology-based phylogenetic fossil placement under Maximum Likelihood

Alexandros Stamatakis, Simon A. Berger, A. Stamatakis, 2010, ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010.

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library

Solon P. Pissis, Alexandros Stamatakis, Nikolaos S. Alachiotis, 2013, 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum.

libgapmis: extending short-read alignments

Solon P. Pissis, Alexandros Stamatakis, Nikolaos S. Alachiotis, 2013, BMC Bioinformatics.

Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code

Alexandros Stamatakis, Wayne Pfeiffer, A. Stamatakis, 2010, 2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW).

Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning

Sebastian Schlag, Alexandros Stamatakis, Benoit Morel, 2019, 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

Uncovering Hidden Phylogenetic Consensus in Large Data Sets

Alexandros Stamatakis, Krister M. Swenson, Bernard M. E. Moret, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Proceedings of the 2013 IEEE 27th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum

Solon P. Pissis, Alexandros Stamatakis, Nikolaos Alachiotis, 2013, IPDPS 2013.

Initial Experiences Porting a Bioinformatics Application to a Graphics Processor

Pedro Trancoso, Alexandros Stamatakis, Maria Charalambous, 2005, Panhellenic Conference on Informatics.

A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits

Alexandros Stamatakis, Jaime Huerta-Cepas, Lucas Czech, 2016 .

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

Benoit Morel, Alexandros Stamatakis, Simon Penel, 2020, Bioinform..

Two C++ libraries for counting trees on a phylogenetic terrace

Alexandros Stamatakis, M. Hamann, F. Weber, 2018, Bioinform..

A fast and memory-efficient implementation of the transfer bootstrap

Alexey M. Kozlov, Alexandros Stamatakis, Alexey M Kozlov, 2019, bioRxiv.

The AxML program family for maximum likelihood‐based phylogenetic tree inference

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2004, Concurr. Pract. Exp..

Boosting the Performance of Bayesian Divergence Time Estimation with the Phylogenetic Likelihood Library

Alexandros Stamatakis, Tomás Flouri, Diego Darriba, 2013, 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum.

ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models

Alexandros Stamatakis, Benoit Morel, David Posada, 2019 .

The divisible load balance problem with shared cost and its application to phylogenetic inference

Alexandros Stamatakis, Kassian Kobert, Constantin Scholl, 2016 .

The Divisible Load Balance Problem and Its Application to Phylogenetic Inference

Alexandros Stamatakis, Tomás Flouri, Kassian Kobert, 2014, WABI.

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2005, Bioinform..

A Simple and Accurate Method for Rogue Taxon Identification

Alexandros Stamatakis, Andre J. Aberer, A. Stamatakis, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

Fine-grain Parallelism Using Multi-core, Cell/BE, and GPU Systems: Accelerating the Phylogenetic Likelihood Function

Pedro Trancoso, Alexandros Stamatakis, Frederico Pratas, 2009, 2009 International Conference on Parallel Processing.

Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L

Srinivas Aluru, Alexandros Stamatakis, Michael Ott, 2007, Proceedings of the 2007 ACM/IEEE Conference on Supercomputing (SC '07).

Inferring Phylogenies with RAxML-VI-HPC

Alexandros Stamatakis, A. Stamatakis, 2006 .

Load Balance in the Phylogenetic Likelihood Kernel

Alexandros Stamatakis, Michael Ott, A. Stamatakis, 2009, 2009 International Conference on Parallel Processing.

Adapting PAxML to the Hitachi SR8000-F1 Supercomputer

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2003 .

A simple method for computing all subtree repeats in unordered trees in linear time

Solon P. Pissis, Alexandros Stamatakis, Kassian Kobert, 2012 .

Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges

Alexandros Stamatakis, 2018 .

Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees

Alexandros Stamatakis, Fernando Izquierdo-Carrasco, Stephen A. Smith, 2011, BMC Bioinformatics.

ParBaum: A Fast Program for Phylogenetic Tree Inference with Maximum Likelihood

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2005 .

Efficient PC-FPGA Communication over Gigabit Ethernet

Alexandros Stamatakis, Nikolaos Alachiotis, Simon A. Berger, 2010, 2010 10th IEEE International Conference on Computer and Information Technology.

Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study

Alexandros Stamatakis, Michael Ott, A. Stamatakis, 2008, PRIB.

Runtime scheduling of dynamic parallelism on accelerator-based multi-core systems

Alexandros Stamatakis, Dimitrios S. Nikolopoulos, Matthew Curtis-Maury, 2007, Parallel Comput..

RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine

Alexandros Stamatakis, Dimitrios S. Nikolopoulos, Christos D. Antonopoulos, 2007, 2007 IEEE International Parallel and Distributed Processing Symposium.

Parallel Operating System

Rudolf Eigenmann, Davide Sangiorgi, Paul Feautrier, 2011, Encyclopedia of Parallel Computing.

Tool Environments in CORBA-Based Medical High Performance Computing

Thomas Ludwig, Alexandros Stamatakis, Günther Rackl, 2001, PaCT.

Accelerating Parallel Maximum Likelihood-Based Phylogenetic Tree Calculations Using Subtree Equality Vectors

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2002, ACM/IEEE SC 2002 Conference (SC'02).

Efficiently building on-line tools for distributed heterogeneous environments

Thomas Ludwig, Alexandros Stamatakis, Günther Rackl, 2002, Sci. Program..

Assessment of barrier implementations for fine-grain parallel regions on current multi-core architectures

Alexandros Stamatakis, Simon A. Berger, 2010, 2010 IEEE International Conference On Cluster Computing Workshops and Posters (CLUSTER WORKSHOPS).

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Alexey M. Kozlov, Alexandros Stamatakis, Benoit Morel, 2018, bioRxiv.

Parallel Structural Graph Clustering

Alexandros Stamatakis, Stefan Kramer, Madeleine Seeland, 2011, ECML/PKDD.

Two Independent and Highly Efficient Open Source TKF91 Implementations

Sebastian Graf, Alexandros Stamatakis, Nikolai Baudis, 2015 .

Aligning short reads to reference alignments and trees

Alexandros Stamatakis, Simon A. Berger, A. Stamatakis, 2011, Bioinform..

A fast and memory-efficient implementation of the transfer bootstrap

Alexandros Stamatakis, Alexey M Kozlov, Sarah Lutteropp, 2019, Bioinformatics.

Is the Protein Model Assignment problem under linked branch lengths NP-hard?

Alexandros Stamatakis, Kassian Kobert, Jörg Hauser, 2014, Theor. Comput. Sci..

Parallelized phylogenetic post-analysis on multi-core architectures

Alexandros Stamatakis, Nicholas D. Pattengale, Andre J. Aberer, 2010, J. Comput. Sci..

COMPUTING LARGE PHYLOGENIES WITH STATISTICAL METHODS: PROBLEMS AND SOLUTIONS

Alexandros Stamatakis, Harald Meier, T Ludwig, 2004 .

New fast and accurate heuristics for inference of large phylogenetic trees

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2004, 18th International Parallel and Distributed Processing Symposium, 2004. Proceedings..

Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference

Alexandros Stamatakis, Andre J. Aberer, A. Stamatakis, 2013, 2013 IEEE 27th International Symposium on Parallel and Distributed Processing.

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Alexey M. Kozlov, Alexandros Stamatakis, Benoit Morel, 2019, Bioinform..

Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood

Alexandros Stamatakis, Luay Nakhleh, F. Lin, 2005, HPCC.

12 Grand Challenges in Single-Cell Data Science

Alexander Zelikovsky, Fabian J. Theis, Marcel J. T. Reinders, 2019, PeerJ Prepr..

Prediction of missing sequences and branch lengths in phylogenomic data

Alexandros Stamatakis, Michael Weiß, Diego Darriba, 2016, Bioinform..

An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data

Alexandros Stamatakis, Nikolaos S. Alachiotis, Nikolaos Alachiotis, 2012, 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum.

Parallel and Distributed Computation of Large Phylogenetic Trees

Alexandros Stamatakis, 2005 .

A versatile UDP/IP based PC ↔ FPGA communication platform

Alexandros Stamatakis, Nikolaos Alachiotis, Simon A. Berger, 2012, 2012 International Conference on Reconfigurable Computing and FPGAs.

RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs

Thomas Ludwig, Alexandros Stamatakis, Michael Ott, 2005, PaCT.

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel

Alexandros Stamatakis, Nikolaos Alachiotis, Simon A. Berger, 2011, BMC Bioinformatics.

RAxML‐II: a program for sequential, parallel and distributed inference of large phylogenetic trees

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2005, Concurr. Comput. Pract. Exp..

MoTeX: A word-based HPC tool for MoTif eXtraction

Solon P. Pissis, Alexandros Stamatakis, Pavlos Pavlidis, 2013, BCB.

Bootstrapping (Bootstrap Analysis)

Aidan Budd, Alexandros Stamatakis, 2014 .

A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation

Alexandros Stamatakis, Tomás Flouri, Arndt von Haeseler, 2016, 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE).

Large-scale phylogenetic analysis on current HPC architectures

Srinivas Aluru, Alexandros Stamatakis, Michael Ott, 2008 .

A Novel Heuristic for Data Distribution in Massively Parallel Phylogenetic Inference Using Site Repeats

Alexandros Stamatakis, Benoit Morel, Tomás Flouri, 2017, 2017 IEEE 19th International Conference on High Performance Computing and Communications; IEEE 15th International Conference on Smart City; IEEE 3rd International Conference on Data Science and Systems (HPCC/SmartCity/DSS).

Two C++ Libraries for Counting Trees on a Phylogenetic Terrace

Alexandros Stamatakis, Michael Hamann, Tobias Ribizel, 2017 .

The Divisible Load Balance Problem with Shared Cost and Its Application to Phylogenetic Inference

Alexandros Stamatakis, Tomás Flouri, Kassian Kobert, 2016, 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

Parallel Random Access Machines (PRAM)

Rudolf Eigenmann, Davide Sangiorgi, Paul Feautrier, 2011, Encyclopedia of Parallel Computing.

Efficient floating-point logarithm unit for FPGAs

Alexandros Stamatakis, Nikolaos Alachiotis, 2010, 2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW).

Parallel I/O Library (PIO)

Rudolf Eigenmann, Davide Sangiorgi, Paul Feautrier, 2011, Encyclopedia of Parallel Computing.

Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling

Alexandros Stamatakis, Markus Göker, Guido W. Grimm, 2010, Evolutionary bioinformatics online.

Does the choice of nucleotide substitution models matter topologically?

Alexandros Stamatakis, Michael Hoff, Stefan Orf, 2016, BMC Bioinformatics.

Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions

David A. Bader, Alexandros Stamatakis, Usman Roshan, 2006, Adv. Comput..

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Alexey M. Kozlov, Alexandros Stamatakis, Benoit Morel, 2018 .

Root Digger: a root placement program for phylogenetic trees

Alexandros Stamatakis, Ben Bettisworth, 2021, BMC Bioinform..

Swarm v3: towards tera-scale amplicon clustering

Alexandros Stamatakis, Lucas Czech, Torbjørn Rognes, 2021, Bioinform..

Efficient Memory Management in Likelihood-based Phylogenetic Placement

Alexandros Stamatakis, Pierre Barbera, A. Stamatakis, 2021, 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, 2018, bioRxiv.

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Christina Boucher, Olivier Gascuel, Guy Baele, 2020, Proceedings of the National Academy of Sciences.

RAxML: A Parallel Program for Phylogenetic Tree Inference

Thomas Ludwig, Alexandros Stamatakis, Harald Meier, 2003 .

A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences

Alexandros Stamatakis, Guido W. Grimm, Susanne S. Renner, 2006 .

Using RAxML to Infer Phylogenies

Alexandros Stamatakis, A. Stamatakis, 2015, Current protocols in bioinformatics.

HIV-1 Full-Genome Phylogenetics of Generalized Epidemics in Sub-Saharan Africa: Impact of Missing Nucleotide Characters in Next-Generation Sequences

Astrid Gall, Alexey M. Kozlov, Alexandros Stamatakis, 2017, AIDS research and human retroviruses.

Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context.

Alexandros Stamatakis, Stéphane Audic, Thorsten Stoeck, 2014, Molecular biology and evolution.

Efficient Maximum Likelihood Tree Building Methods

Alexey M. Kozlov, Alexandros Stamatakis, A. Stamatakis, 2020 .

Multiple evolutionary mechanisms drive papillomavirus diversification.

Alexandros Stamatakis, Eggert Stockfleth, A. Stamatakis, 2007, Molecular biology and evolution.

PaPaRa 2 . 0 : A Vectorized Algorithm for Probabilistic Phylogeny-Aware Alignment Extension

Alexandros Stamatakis, Simon A. Berger, 2012 .

Biggest challenges in bioinformatics

Aidan Budd, Alexandros Stamatakis, Kristoffer Forslund, 2013, EMBO reports.

A Nuclear Ribosomal DNA Phylogeny of Acer Inferred with Maximum Likelihood, Splits Graphs, and Motif Analysis of 606 Sequences

Alexandros Stamatakis, Guido W. Grimm, Susanne S. Renner, 2006, Evolutionary bioinformatics online.

Tree Topology

Aidan Budd, Alexandros Stamatakis, 2010 .

Phylogenetic Search Algorithms for Maximum Likelihood

Alexandros Stamatakis, A. Stamatakis, 2010 .

Minimising processor communication in parallel approximate string matching

Costas S. Iliopoulos, Solon P. Pissis, Alexandros Stamatakis, 2012 .

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

Alexandros Stamatakis, Denis Krompass, Andre J. Aberer, 2012, Systematic biology.

The State of Software for Evolutionary Biology

Alexandros Stamatakis, Diego Darriba, Tomáš Flouri, 2018, Molecular biology and evolution.

A Functional Phylogenomic View of the Seed Plants

Alexandros Stamatakis, Michael Ott, Gloria Coruzzi, 2011, PLoS genetics.

A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits

Alexandros Stamatakis, Jaime Huerta-Cepas, Lucas Czech, 2017, Molecular biology and evolution.

Taxon sampling versus computational complexity and their impact on obtaining the Tree of Life

Alexandros Stamatakis, Olaf R. P. Bininda-Emonds, A. Stamatakis, 2007 .

A daily-updated tree of (sequenced) life as a reference for genome research

Alexandros Stamatakis, Hai Fang, Julian Gough, 2013, Scientific Reports.

Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples

Alexandros Stamatakis, Lucas Czech, A. Stamatakis, 2019, PloS one.

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

Alexandros Stamatakis, Adam D. Leaché, Joseph Felsenstein, 2015, Systematic biology.

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

Alexandros Stamatakis, Kassian Kobert, Andre J. Aberer, 2014, Molecular biology and evolution.

The RAxML 7.0.3 Manual

Alexandros Stamatakis, A. Stamatakis, The Exelixis Lab, 2008 .

The RAxML v 8 . 1 . X Manual by Alexandros Stamatakis

Alexandros Stamatakis, A. Stamatakis, 2014 .

Phylogeny-aware identification and correction of taxonomically mislabeled sequences

Pelin Yilmaz, Frank Oliver Glöckner, Alexey M. Kozlov, 2016, bioRxiv.

Novel information theory-based measures for quantifying incongruence among phylogenetic trees.

Alexandros Stamatakis, Antonis Rokas, Leonidas Salichos, 2014, Molecular biology and evolution.

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

Alexandros Stamatakis, Karen Meusemann, Bui Quang Minh, 2013, Molecular biology and evolution.

Understanding Angiosperm Diversification Using Small and Large Phylogenetic Trees 1

Alexandros Stamatakis, M. Donoghue, Stephen A. Smith, 2022 .

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, 2020, bioRxiv.

The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data

Alexandros Stamatakis, Karen Meusemann, Oliver Niehuis, 2014, BMC Evolutionary Biology.

Message from the workshop chairs

Srinivas Aluru, Nagiza F. Samatova, Albert Y. Zomaya, 2009 .

An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees

Alexandros Stamatakis, Fredrik Ronquist, Andre J. Aberer, 2015, Systematic biology.

Metagenomic species profiling using universal phylogenetic marker genes

Alexandros Stamatakis, Peer Bork, Søren Brunak, 2013, Nature Methods.