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Two Independent and Highly Efficient Open Source TKF91 Implementations

Abstract (Expand)

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.

Authors: Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp, Daniel Opitz, Tomas Flouri, Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

Do Phylogenetic Tree Viewers correctly display Support Values?

Abstract

Not specified

Authors: Lucas Czech, Alexandros Stamatakis

Date Published: 2015

Publication Type: Journal

Transition Path Sampling with Quantum/Classical Mechanics for Reaction Rates

Abstract

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Authors: Frauke Gräter, Wenjin Li

Date Published: 2015

Publication Type: InCollection

A proton relay enhances H2O2 sensitivity of GAPDH to facilitate metabolic adaptation

Abstract

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Authors: David Peralta, Agnieszka K Bronowska, Bruce Morgan, Éva Dóka, Koen Van Laer, Péter Nagy, Frauke Gräter, Tobias P Dick

Date Published: 2015

Publication Type: Journal

A fast recoiling silk-like elastomer facilitates nanosecond nematocyst discharge

Abstract

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Authors: Anna Beckmann, Senbo Xiao, Jochen P Müller, Davide Mercadante, Timm Nüchter, Niels Kröger, Florian Langhojer, Wolfgang Petrich, Thomas W Holstein, Martin Benoit, others

Date Published: 2015

Publication Type: Journal

Allosteric Regulation of Focal Adhesion Kinase by PIP 2 and ATP

Abstract

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Authors: Jing Zhou, Agnieszka Bronowska, Johanne Le Coq, Daniel Lietha, Frauke Gräter

Date Published: 2015

Publication Type: Journal

Redox Potentials of Protein Disulfide Bonds from Free-Energy Calculations

Abstract

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Authors: Wenjin Li, Ilona B. Baldus, Frauke Gräter

Date Published: 2015

Publication Type: Journal

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