I have a dataset of 6 microsats loci from 11 populations of a barnacle. I’d need 100-1000 matrices of pairwise Fst-values, in order to carry out a spatial analysis. Is there any software producing these bootstrapped matrices?
Thanks Saul. I used ADEGENET, but I didn't remember the possibility to make bootstrapped Fst matrices.
Kevin, thank you for your detailed answer. What I need is a txt file with a vertical sequence of N (let's say N=100 to 1000) bootstrapped lower triangular matrices of pairwise Fst. As regards the point 2 you raised, I usually take into account uncorrected matrices, but it would be interesting to use the corrected matrices as well and compare the 2 outcomes.
Kevin, I used the function you sent me in diveRsity. It's ok! It works. I used the file with 1000 bootstrap matrices of corrected and uncorrected pairwise Fst values, in order to detect barriers within the dataset by applying the Monmonier's algorithm. Corrected and uncorrected Fst valus gave identical results. Thanks again. Ciao. Ferruccio.
you can use MSA (Microsatellite Analyzer; free download at: http://i122server.vu-wien.ac.at/MSA/MSA_download.html).
MSA (Microsatellite Analyzer; free download at: http://i122server.vu-wien.ac.at/MSA/MSA_download.html).
#Ghasem Askari would you mind sharing the MSA software. I tried the link you gave but not downloading. My email is [email protected]
Thanks in advance
Collins
Does anyone encourage problems running DiveRsity/wrireBoot function in R??? I used it successfully several months ago, and now it constantly report error:
> writeBoot(infile = data_genepop, outfile = "23032017_10_boot", gp = 3, bootstraps = 10, parallel = F)
Error in data1[data1 == 0]
I had some troubles running diveRsity::writeBoot.
Parallel argument must be set to TRUE. parallel = FALSE causes problems.
Also, diveRsity::basicStats and diveRsity::diffCalc ran my data. However, I had to make minor adjustments to my data (remove some empty spaces) to run writeBoot.
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