tiagoantao/genomics-notebooks

IPython notebooks to teach Genomics and Population Genetics

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Books

Fast Python - Writing efficient Python code. Repository here

Bioinformatics with Python Cookbook - third edition - Python for Bioinformatics. Repository here

genomics-notebooks's Issues

List of requests

"7.1 . Using simulations determine what is the effect Ne on rate of loss of Heterozytosity? If the initial allele frequency is 0.5 (at each of 100 loci), how many generations does it take for He to to go to zero if Ne is 10 versus 50 versus 500? How does this chance if the initial allele frequency is 0.2? Bonus: do you know what the typical or average heterozygosity of a SNP (or minor allele frequency or initial allele frequency) used in studies in most natural populations?

7.8. Use simulations to understand the power of LDNe estimator to estimate Nb.

9.10. Simulate to assess the interaction between drift and gene flow. How many generations does it take for genetically-distinct clusters to evolve (as visualized by PCA) when Ne is 10 versus 50, and also when Nm is 0 versus 1 (for both Ne of 10 and 50)? Use 10 loci and then 100 and report the difference in time (generations) for clusters to evolve.

Repeat the analysis using Structure (and bar plots from Structure)"