Understanding how e.g. humans got neanderthal genes requires understanding hybridisation. Ongoing hybridisation is common in nature. A central analysis is of change in allele frequencies across field areas (clines), and this analysis is well established and tested. However: Software for those analyses does not yet leverage the power of multiple processor cores. The project is to update one such software: 'Analyse' to 'coreAnalyse'.

Tasks:

1. Multi-core Python implementation of the Analyse cline likelihood function. The student will study the principles of likelihood and clinal analysis. The student will demonstrate a Python grid search of likelihood calculations contrasting single vs multiple core use.
2. Hdf5 file storage of intermediate 6-8 dimensional datamatrices The student will study the Hdf5 data storage format. The student will design and demonstrate an Hdf5 usage for likelihood grid search results.
3. User-friendly summarisation of maxima across axes of those matrices The student will use their grid search and Hdf5 design to analyse a real-world hybrid zone dataset. They will summarise the output using software of their choice.

Literature

Szymura, Jacek M., and Nicholas H. Barton. "The genetic structure of the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata: comparisons between transects and between loci." Evolution 45.2 (1991): 237-261.

Barton, N. H., and S. J. E. Baird. "Analyse: an application for analysing hybrid zones." Freeware, Edinburgh, UK (1995).

Baird, S. J. E., Petružela, J., Jaroň, I., Škrabánek, P., Martínková, N. (2022). Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution, 00, 0-17. https://doi.org/10.1111/2041-210X.14010