PT - JOURNAL ARTICLE AU - Nikolai Baudis AU - Pierre Barbera AU - Sebastian Graf AU - Sarah Lutteropp AU - Daniel Opitz AU - Tomáš Flouri AU - Alexandros Stamatakis TI - Two Independent and Highly Efficient Open Source TKF91 Implementations AID - 10.1101/033191 DP - 2015 Jan 01 TA - bioRxiv PG - 033191 4099 - http://biorxiv.org/content/early/2015/11/29/033191.short 4100 - http://biorxiv.org/content/early/2015/11/29/033191.full 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.