Hey,
I am working in population genetics. I used DNAsp to convert fasta into .arp file for input in Arlequin. Can anyone help to interpret the data in the .arp file? As in which column represents what? My data looks like the one attached.
Is there any other way to know the haplotype of an snp (rs id known)
Thank You.
Have you looked at the manual for Arlequin? http://cmpg.unibe.ch/software/arlequin35/man/Arlequin35.pdf
See Section 4
You have 48 sequences. 3 of these are identical =Hap_1, (meaning haplotype 1).
Next, 17 sequences are identical =Hap_2
And so on
All in all your sequences can be divided into 9 different groups, each with a different number of identical sequences, emanating from 48 different samples. Whether these are from nine different species or just represent slight intraspecific variation can not be determined from this table.
@Urban Olsson thank you so much for the clear interpretation.
@Tyler Chaffin....will surely go through it once.
Thank you.
@Urban Olsson can you suggest any software or methods to infer more information regarding the haplotype an SNP belongs to? For example I have a list of SNPs and I want to know which haplotype so each belong, so how do I go about that?
As mentioned by Das, u can check the details of Haplotype types in the Dnasp. And if you want to further draw a haplotype network, u can export it to Network software for analysis.
I suggest you first look at DnaSP manual and read about SNP section, then consider information on haplotypes about your data
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