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Two Independent and Highly Efficient Open Source TKF91 Implementations

Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp, Daniel Opitz, Tomáš Flouri, Alexandros Stamatakis
doi: https://doi.org/10.1101/033191
Nikolai Baudis
1Karlsruhe Institute of Technology, Institute of Theoretical Informatics, Karlsruhe, Germany
2Heidelberg Institute for Theoretical Studies, Scientic Computing Group, Heidelberg, Germany
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Pierre Barbera
1Karlsruhe Institute of Technology, Institute of Theoretical Informatics, Karlsruhe, Germany
2Heidelberg Institute for Theoretical Studies, Scientic Computing Group, Heidelberg, Germany
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Sebastian Graf
1Karlsruhe Institute of Technology, Institute of Theoretical Informatics, Karlsruhe, Germany
2Heidelberg Institute for Theoretical Studies, Scientic Computing Group, Heidelberg, Germany
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Sarah Lutteropp
1Karlsruhe Institute of Technology, Institute of Theoretical Informatics, Karlsruhe, Germany
2Heidelberg Institute for Theoretical Studies, Scientic Computing Group, Heidelberg, Germany
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Daniel Opitz
1Karlsruhe Institute of Technology, Institute of Theoretical Informatics, Karlsruhe, Germany
2Heidelberg Institute for Theoretical Studies, Scientic Computing Group, Heidelberg, Germany
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Tomáš Flouri
1Karlsruhe Institute of Technology, Institute of Theoretical Informatics, Karlsruhe, Germany
2Heidelberg Institute for Theoretical Studies, Scientic Computing Group, Heidelberg, Germany
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Alexandros Stamatakis
1Karlsruhe Institute of Technology, Institute of Theoretical Informatics, Karlsruhe, Germany
2Heidelberg Institute for Theoretical Studies, Scientic Computing Group, Heidelberg, Germany
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Abstract

In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by Thorne, Kishino, and Felsenstein in 1991. This paper has two parts. In the educational part, we cover teaching issues regarding the setup of the course and the practical and summarize student and teacher experiences. In the scientific part, the two student teams (Team I: Nikolai, Sebastian, Daniel; Team II: Sarah, Pierre) present their solutions for implementing efficient and numerically stable implementations of the TKF91 algorithm. The two teams worked independently on implementing the same algorithm. Hence, since the implementations yield identical results —with slight numerical deviations— we are confident that the implementations are correct. We describe the optimizations applied and make them available as open-source codes in the hope that our findings and software will be useful to the community as well as for similar programming practicals at other universities.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted November 29, 2015.
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Two Independent and Highly Efficient Open Source TKF91 Implementations
Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp, Daniel Opitz, Tomáš Flouri, Alexandros Stamatakis
bioRxiv 033191; doi: https://doi.org/10.1101/033191
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Two Independent and Highly Efficient Open Source TKF91 Implementations
Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp, Daniel Opitz, Tomáš Flouri, Alexandros Stamatakis
bioRxiv 033191; doi: https://doi.org/10.1101/033191

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