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- Title
Implementation of a Stirling number estimator enables direct calculation of population genetics tests for large sequence datasets.
- Authors
Chen, Swaine L
- Abstract
Motivation Stirling numbers enter into the calculation of several population genetics statistics, including Fu's F s. However, as alignments become large (≥50 sequences), the Stirling numbers required rapidly exceed the standard floating point range. Another recursive method for calculating Fu's F s suffers from floating point underflow issues. Results I implemented an estimator for Stirling numbers that has the advantage of being uniformly applicable to the full parameter range for Stirling numbers. I used this to create a hybrid Fu's F s calculator that accounts for floating point underflow. My new algorithm is hundreds of times faster than the recursive method. This algorithm now enables accurate calculation of statistics such as Fu's F s for very large alignments. Availability and implementation An R implementation is available at http://github.com/swainechen/hfufs. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
POPULATION genetics; POPULATION statistics; SEQUENCE alignment
- Publication
Bioinformatics, 2019, Vol 35, Issue 15, p2668
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bty1012