Hi all!
I was wondering if you can help me about my reasearch I am conducitng. I have a more health oriantated educational background so I lack fromal education in the area of population genetic ( altough we had lessons regarding punnett square and Hardy-Weinber equlibrium). I conducted a research on my own trying to master population genetics via e books and the internet. My work is in investigating a simple bi alellic locus via RFLP in wich the ancestral allele looks like a single band on gel because he lacks the mutated SNP and the other allel the derived one gets cut in to two unequal halves.
Now my goal is to compare my results with world wide populations using ALFRED data base. I have only raw data on my population ( I know who is a homozygote and heteroygote for a particular alelle) but the populations I am comparing to have only relative allele frequencys so I can use only specific bioinformatic softwares. I did the following:
Intrapopulation study
Calculating allele and genotype freq ( Genalex)
Hard-Weinberg test ( chi square test and fixation indeks ( Genalex)
Interpopulation studies
Paiwise Fst ( Arelquin)
Genetic distance Nei Da and Dst ( Poptree2w)
AMOVA Fst for groups of populations ( I have grouped my population vith other European populatiosn and did the same with populations from other continets so I could make groups)
Z test for 2 proprtions to chekc if the allele frequency of the ancestral type differs greatly from the frequency of the same allele in other european populations clustered in one big group
Neignhbour joining usin genetic distance ( MEGA)
PC principal component analysis using allele freq( PAST3)
Non metric multidimensional scaling using allele freq and euclidian distance ( PAST3)
Have I choosen the right methods or are there other methods some of you would perhaps have used.
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