Questions tagged [populations]

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How to open .weir.fst files witout losing data?

I have .vcf file with over 78 000 variations in 95 experiment subjects. I used vcftools to extract fixation index score for general differentiation between Case and Control groups. ...
Lukas Chumchal's user avatar
2 votes
0 answers
26 views

Calculation of Site Frequency Spectrum (SFS) using STR data

Hi everyone I had a question on if it is possible to calculate (Site Frequency Spectrum)SFS using STR data. Please mention if you know any programm that can be used for that! I have tried Arlequin but ...
George X.'s user avatar
3 votes
1 answer
39 views

Is there a way I can combine geological data with population genetics data?

So I have ran SAMOVA and made calculations regarding haplotype diversity and nucleotide diversity of several populations. I have also made raster data regarding geographical data like slope, ...
Nickmofoe's user avatar
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2 votes
1 answer
74 views

How can I fix "Ill-defined genetic structure" Error message in Arlequin?

I am performing an AMOVA analysis via Arlequin. At this point, I have: collected sequences of mtDNA from the cox1 gene, aligned the different genes using clustalX converted the files into .arp ...
Nickmofoe's user avatar
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1 vote
1 answer
43 views

How can I use sequences with different lengths in arlequin?

I have mtDNA sequences of the cox1 gene from various populations of one species. I want to perform an AMOVA allele frequency analysis via Arlequin. This allele frequency package however requires my ...
Nickmofoe's user avatar
  • 339
3 votes
2 answers
109 views

How can I resolve "missing name of population" message in PGDSpider?

I want to use Arlequin for AMOVA. I have my FASTA files which I want to convert into .arp files which are recognizable by arlequin. When I try to convert it using Population Genetics Data (format) ...
Nickmofoe's user avatar
  • 339