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1

Tree template matching in ranked ordered trees by pushdown automata

Flouri, Tomáš, Iliopoulos, Costas S., Janoušek, Jan, Melichar, Bořivoj, Pissis, Solon P.

Journal:

Journal of Discrete Algorithms

Year:

2012

Language:

english

File:

PDF, 639 KB

english, 2012

2

[IEEE 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Hong Kong, China (2010.12.18-2010.12.21)] 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - An algorithm for mapping short reads to a dynamically changing genomic sequence

Flouri, Tomas, Holub, Jan, Iliopoulos, Costas, Pissis, Solon

Year:

2010

Language:

english

File:

PDF, 375 KB

english, 2010

3

Computing all subtree repeats in ordered trees

Christou, Michalis, Crochemore, Maxime, Flouri, Tomáš, Iliopoulos, Costas S., Janoušek, Jan, Melichar, Bořivoj, Pissis, Solon P.

Journal:

Information Processing Letters

Year:

2012

Language:

english

File:

PDF, 166 KB

english, 2012

4

Tree template matching in unranked ordered trees

Christou, Michalis, Flouri, Tomáš, Iliopoulos, Costas S., Janoušek, Jan, Melichar, Bořivoj, Pissis, Solon P., Žďárek, Jan

Journal:

Journal of Discrete Algorithms

Year:

2013

Language:

english

File:

PDF, 492 KB

english, 2013

5

Enhanced string covering

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

Journal:

Theoretical Computer Science

Year:

2013

Language:

english

File:

PDF, 656 KB

english, 2013

6

libgapmis: extending short-read alignments

Alachiotis, Nikolaos, Berger, Simon, Flouri, Tomáš, Pissis, Solon P, Stamatakis, Alexandros

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 1.20 MB

english, 2013

7

[IEEE 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW) - Cambridge, MA, USA (2013.05.20-2013.05.24)] 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum - Boosting the Performance of Bayesian Divergence Time Estimation with the Phylogenetic Likelihood Library

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

Year:

2013

Language:

english

File:

PDF, 292 KB

english, 2013

8

[IEEE 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW) - Cambridge, MA, USA (2013.05.20-2013.05.24)] 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum - A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library

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

Year:

2013

Language:

english

File:

PDF, 202 KB

english, 2013

9

[IEEE 2009 International Multiconference on Computer Science and Information Technology (IMCSIT) - Mragowo, Poland (2009.10.12-2009.10.14)] 2009 International Multiconference on Computer Science and Information Technology - Subtree matching by deterministic pushdown automata

Flouri, Tomas, Melichar, Borivoj, Janousek, J.

Year:

2009

Language:

english

File:

PDF, 151 KB

english, 2009

10

[IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Philadelphia, USA (2012.10.4-2012.10.7)] 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops - Libgapmis: An ultrafast library for short-read single-gap alignment

Alachiotis, Nikolaos, Berger, Simon, Flouri, Tomas, Pissis, Solon P., Stamatakis, Alexandras

Year:

2012

Language:

english

File:

PDF, 877 KB

english, 2012

11

Global and local sequence alignment with a bounded number of gaps

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

Journal:

Theoretical Computer Science

Year:

2015

Language:

english

File:

PDF, 1.15 MB

english, 2015

12

[ACM Press the 2nd ACM Conference - Chicago, Illinois (2011.08.01-2011.08.03)] Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11 - Approximate string-matching with a single gap for sequence alignment

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

Year:

2011

Language:

english

File:

PDF, 592 KB

english, 2011

13

[ACM Press the International Conference - Wshington DC, USA (2013.09.22-2013.09.25)] Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13 - GapsMis

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

Year:

2007

Language:

english

File:

PDF, 269 KB

english, 2007

14

[ACM Press the 2nd ACM Conference - Chicago, Illinois (2011.08.01-2011.08.03)] Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11 - DynMap

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

Year:

2011

Language:

english

File:

PDF, 639 KB

english, 2011

15

[ACM Press the 2010 ACM Symposium - Sierre, Switzerland (2010.03.22-2010.03.26)] Proceedings of the 2010 ACM Symposium on Applied Computing - SAC '10 - Aho-Corasick like multiple subtree matching by pushdown automata

Flouri, Tomáš, Melichar, Bořivoj, Janoušek, Jan

Year:

2010

Language:

english

File:

PDF, 241 KB

english, 2010

16

Longest common substrings with k mismatches

Flouri, Tomas, Giaquinta, Emanuele, Kobert, Kassian, Ukkonen, Esko

Journal:

Information Processing Letters

Year:

2015

Language:

english

File:

PDF, 251 KB

english, 2015

17

[IEEE 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE) - Hanoi, Vietnam (2016.10.6-2016.10.8)] 2016 Eighth International Conference on Knowledge and Systems Engineering (KSE) - A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation

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

Year:

2016

Language:

english

File:

PDF, 761 KB

english, 2016

18

[IEEE 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) - Chicago, IL, USA (2016.5.23-2016.5.27)] 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) - The Divisible Load Balance Problem with Shared Cost and Its Application to Phylogenetic Inference

Scholl, Constantin, Kobert, Kassian, Flouri, Toma, Stamatakis, Alexandros

Year:

2016

Language:

english

File:

PDF, 335 KB

english, 2016

19

The state of software for evolutionary biology

Darriba, Diego, Flouri, Tomáš, Stamatakis, Alexandros

Journal:

Molecular Biology and Evolution

Year:

2018

Language:

english

File:

PDF, 386 KB

english, 2018

20

MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation

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

Journal:

BMC Evolutionary Biology

Year:

2018

Language:

english

File:

PDF, 1.37 MB

english, 2018

21

[IEEE 2017 IEEE 19th International Conference on High Performance Computing and Communications, IEEE 15th International Conference on Smart City and IEEE 3rd International Conference on Data Science and Systems (HPCC/SmartCity/DSS) - Bangkok (2017.12.18-2017.12.20)] 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) - A Novel Heuristic for Data Distribution in Massively Parallel Phylogenetic Inference Using Site Repeats

Morel, Benoit, Flouri, Tomas, Stamatakis, Alexandros

Year:

2017

Language:

english

File:

PDF, 298 KB

english, 2017

22

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

Kozlov, Alexey M, Darriba, Diego, Flouri, Tomáš, Morel, Benoit, Stamatakis, Alexandros, Wren, Jonathan

Journal:

Year:

2019

Language:

english

File:

PDF, 173 KB

english, 2019

23

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

Darriba, Diego, Posada, David, Kozlov, Alexey M, Stamatakis, Alexandros, Morel, Benoit, Flouri, Tomas, Crandall, Keith

Journal:

Molecular Biology and Evolution

Year:

2019

Language:

english

File:

PDF, 297 KB

english, 2019

24

[AIP COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING: Theory and Computation: Old Problems and New Challenges. Lectures Presented at the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007): VOLUME 1 - ()] AIP Conference Proceedings - Indexing Degenerate Strings

Voráček, Michal, Vagner, Ladislav, Flouri, Tomáš, Simos, Theodore E., Maroulis, George

Year:

2007

Language:

english

File:

PDF, 993 KB

english, 2007

25

An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola)

Vasilikopoulos, Alexandros, Misof, Bernhard, Meusemann, Karen, Lieberz, Doria, Flouri, TomÃ¡Å¡, Beutel, Rolf G., Niehuis, Oliver, Wappler, Torsten, Rust, Jes, Peters, Ralph S., Donath, Alexander, Pods

Journal:

BMC Evolutionary Biology

Year:

2020

File:

PDF, 3.48 MB

2020

26

A simulation study to examine the information content in phylogenomic datasets under the multispecies coalescent model

Huang, Jun, Flouri, TomÃ¡Å¡, Yang, Ziheng, Su, Bing

Journal:

Molecular Biology and Evolution

Year:

2020

File:

PDF, 964 KB

2020

27

Correction to: An integrative phylogenomic approach to elucidate the evolutionary history and divergence times of Neuropterida (Insecta: Holometabola)

Vasilikopoulos, Alexandros, Misof, Bernhard, Meusemann, Karen, Lieberz, Doria, Flouri, TomÃ¡Å¡, Beutel, Rolf G., Niehuis, Oliver, Wappler, Torsten, Rust, Jes, Peters, Ralph S., Donath, Alexander, Pods

Journal:

BMC Evolutionary Biology

Year:

2020

File:

PDF, 1.27 MB

2020