Tue 20.11, 14-18, C128
THIS IS EXAM MATERIAL
• Review: Estimating population genetic structures.pdf
• Review: Data analysis methods.pdf
• Home-exercise 3.pdf, Appendix to Home-exercise 3.pdf
Home-exercise 3 was done during the session. During the session Wed 28.11 more background theory.
Data to be analysed:
Tajima D calculator
Human population HLA-gene data: Zulu.txt, Toroko.txt, Sioux.txt, South Indian.txt, Mexican.txt, Irish.txt, Filipino.txt, Zulu.txt, Czech.txt, Finn 90.txt, Turk.txt
Bacteria data: USA_before_vacc.txt, USA_after_vacc.txt, Skand_before_vacc.txt, Skand_after_vacc.txt
Selecton server, Selecton tutorial.pdf
Growth hormone gene.txt, BDNF-gene.txt, HLA gene.txt
Wed 21.11, 14-18, C128.
NOT FOR EXAM (This is 1cr in addition to the 4cr from the course, cf. this: More information here.pdf)
Guidance to practical work in computer class.
Data-analysis by the software Arlequin3.5, Manual
Example data for training during the session, which is aloso part A for the assignment:
HLA_DRB1_freqtable.xlsx, HLA_DRB1_seqs.txt The script: convertToArlequin.R.txt, Completed data_file to Arlequin.txt, Script comments.txt
This is geographical population data from one very polymorphic human gene (very many alleles, the sequences), collected from here
Arlequin assignment.pdf, Example 1.pdf, Example 2.pdf
Note added 3.12: I have now corrected the datafile which included mistakes in the data-collection step. The inputfile, which you should name again as .arp, instead of .txt, works fine.