RT Journal Article
SR Electronic
T1 Two Independent and Highly Efficient Open Source TKF91 Implementations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 033191
DO 10.1101/033191
A1 Nikolai Baudis
A1 Pierre Barbera
A1 Sebastian Graf
A1 Sarah Lutteropp
A1 Daniel Opitz
A1 Tomáš Flouri
A1 Alexandros Stamatakis
YR 2015
UL http://biorxiv.org/content/early/2015/11/29/033191.abstract
AB 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.