Biol 5221: Human Evolutionary Genetics Lab

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Lab syllabus  [08 January 2024 12:37:07.] 

Just Enough Python  [17 January 2024 11:39:27.] 

Lab manual  [22 April 2024 14:40:10.] 

Example lab report  [11 February 2022 17:38:07.] 

Data

• HapMap ftp site
• Encode SNPs from region 7q31 of human chromosome 7
• Short version preceding file, containing just four SNPs. (For debugging.)
• genotypes_chr99_CEU_r23a_nr.b36_fwd.txt Shortened version the HapMap file for chromosome 2, population CEU. (For debugging.)

Matplotlib Tutorial and Code

Matplotlib is a Python package for graphics. It isn't required for this course, but you are welcome to use it. The graphics it makes are much better than the character-based graphics provided by pgen.py. The links below contain documentation and sample code. They were provided by Todd Islam.

• Documentation
• Code

Computer Programs

• pgen.py, a Python module that includes classes for accessing and manipulating HapMap data.
• Wolf_2_incomplete.py Simulate Wolf's dice.
• drift.py Forward time simulation of drift.
• coal_depth.py Coalescent simulation of genetic drift.
• cointest.py Use simulation to test a hypothesis.
• coin_ci.py Use simulation to generate a confidence interval.
• twolocinc.py Simulate selection, drift, and recombination at two loci. This version is incomplete; it will be completed as part of a lab project.
• haphetinc.py Calculate observed and expected heterozygosity from a sample of HapMap SNPs.
• hapspecinc.py Calculate the site frequency spectrum from HapMap data
• var.py Calculate variances
• snptabinc.py Tabulate data from a pair of adjacent HapMap SNPs, and use these data to estimate linkage disequilibrium.
• rscaninc.py Scan HapMap for LD
• lactaseinc.py Compare LD around lactase gene with that in rest of chromosome 2.