CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data.

ABSTRACT: Statistical tests for molecular evolution provide quantifiable insights into the selection pressures that govern a genome's evolution. Increasing sample sizes used for analysis leads to higher statistical power. However, this requires more computational nodes or longer computational time.CATE (CUDA Accelerated Testing of Evolution) is a computational solution to this problem comprised of two main innovations. The first is a file organization system coupled with a novel search algorithm and the second is a large-scale parallelization of algorithms using both graphical processing unit (GPU) and central processing unit. CATE is capable of conducting evolutionary tests such as Tajima's D, Fu and Li's, and Fay and Wu's test statistics, McDonald-Kreitman Neutrality Index, Fixation Index and Exte

SUBMITTER: Perera D 

PROVIDER: S-EPMC12373131 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature