Tomás Flouri

According to our database, Tomás Flouri authored at least 32 papers between 2008 and 2019.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2019

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

Alexey M. Kozlov, Diego Darriba, Tomás Flouri, Benoit Morel, Alexandros Stamatakis

Bioinform., 2019

2017

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo.

Paschalia Kapli, Sarah Lutteropp, Jiajie Zhang, Kassian Kobert, Pavlos Pavlidis, Alexandros Stamatakis, Tomás Flouri

Bioinform., 2017

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

Benoit Morel, Tomás Flouri, Alexandros Stamatakis

Proceedings of the 19th IEEE International Conference on High Performance Computing and Communications; 15th IEEE International Conference on Smart City; 3rd IEEE International Conference on Data Science and Systems, 2017

An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties.

Tomás Flouri, Jiajie Zhang, Lucas Czech, Kassian Kobert, Alexandros Stamatakis

Proceedings of the Algorithms for Next-Generation Sequencing Data, Techniques, 2017

2016

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

Diep Thi Hoang, Le Sy Vinh, Tomás Flouri, Alexandros Stamatakis, Arndt von Haeseler, Bui Quang Minh

Proceedings of the 2016 Eighth International Conference on Knowledge and Systems Engineering, 2016

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

Constantin Scholl, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis

Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016

2015

Global and local sequence alignment with a bounded number of gaps.

Carl Barton, Tomás Flouri, Costas S. Iliopoulos, Solon P. Pissis

Theor. Comput. Sci., 2015

Longest common substrings with k mismatches.

Tomás Flouri, Emanuele Giaquinta, Kassian Kobert, Esko Ukkonen

Inf. Process. Lett., 2015

2014

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

Jiajie Zhang, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis

Bioinform., 2014

The Divisible Load Balance Problem and Its Application to Phylogenetic Inference.

Kassian Kobert, Tomás Flouri, Andre J. Aberer, Alexandros Stamatakis

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

2013

Enhanced string covering.

Tomás Flouri, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, W. F. Smyth, Wojciech Tyczynski

Theor. Comput. Sci., 2013

Tree template matching in unranked ordered trees.

Michalis Christou, Tomás Flouri, Costas S. Iliopoulos, Jan Janousek, Borivoj Melichar, Solon P. Pissis, Jan Zdárek

J. Discrete Algorithms, 2013

libgapmis: extending short-read alignments.

Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

BMC Bioinform., 2013

An Optimal Algorithm for Computing All Subtree Repeats in Trees.

Tomás Flouri, Kassian Kobert, Solon P. Pissis, Alexandros Stamatakis

Proceedings of the Combinatorial Algorithms - 24th International Workshop, 2013

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

Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

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

Diego Darriba, Andre J. Aberer, Tomás Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis

Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

GapsMis: flexible sequence alignment with a bounded number of gaps.

Carl Barton, Tomás Flouri, Costas S. Iliopoulos, Solon P. Pissis

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

Arbology: Trees and pushdown automata.

Borivoj Melichar, Jan Janousek, Tomás Flouri

Kybernetika, 2012

Tree template matching in ranked ordered trees by pushdown automata.

Tomás Flouri, Costas S. Iliopoulos, Jan Janousek, Borivoj Melichar, Solon P. Pissis

J. Discrete Algorithms, 2012

Computing all subtree repeats in ordered trees.

Michalis Christou, Maxime Crochemore, Tomás Flouri, Costas S. Iliopoulos, Jan Janousek, Borivoj Melichar, Solon P. Pissis

Inf. Process. Lett., 2012

New and Efficient Approaches to the Quasiperiodic Characterisation of a String.

Tomás Flouri, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, William F. Smyth, Wojciech Tyczynski

Proceedings of the Prague Stringology Conference 2012, 2012

GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures.

Tomás Flouri, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis

Proceedings of the Artificial Intelligence Applications and Innovations, 2012

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

Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011

Computing All Subtree Repeats in Ordered Ranked Trees.

Michalis Christou, Maxime Crochemore, Tomás Flouri, Costas S. Iliopoulos, Jan Janousek, Borivoj Melichar, Solon P. Pissis

Proceedings of the String Processing and Information Retrieval, 2011

Tree Indexing by Pushdown Automata and Repeats of Subtrees.

Tomás Flouri, Jan Janousek, Borivoj Melichar, Costas S. Iliopoulos, Solon P. Pissis

Proceedings of the Federated Conference on Computer Science and Information Systems, 2011

Approximate string-matching with a single gap for sequence alignment.

Tomás Flouri, Kunsoo Park, Kimon Frousios, Solon P. Pissis, Costas S. Iliopoulos, German Tischler

Proceedings of the ACM International Conference on Bioinformatics, 2011

DynMap: mapping short reads to multiple related genomes.

Tomás Flouri, Costas S. Iliopoulos, Solon P. Pissis

Proceedings of the ACM International Conference on Bioinformatics, 2011

2010

Subtree matching by pushdown automata.

Tomás Flouri, Jan Janousek, Borivoj Melichar

Comput. Sci. Inf. Syst., 2010

Aho-Corasick like multiple subtree matching by pushdown automata.

Tomás Flouri, Borivoj Melichar, Jan Janousek

Proceedings of the 2010 ACM Symposium on Applied Computing (SAC), 2010

An algorithm for mapping short reads to a dynamically changing genomic sequence.

Tomás Flouri, Jan Holub, Costas S. Iliopoulos, Solon P. Pissis

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009

Subtree matching by deterministic pushdown automata.

Tomás Flouri, Borivoj Melichar, Jan Janousek

Proceedings of the International Multiconference on Computer Science and Information Technology, 2009

2008

Indexing Factors in DNA/RNA Sequences.

Tomás Flouri, Costas S. Iliopoulos, Mohammad Sohel Rahman, Ladislav Vagner, Michal Vorácek

Proceedings of the Bioinformatics Research and Development, 2008