I'm trying to carry out the Mantel test using Arlequin. But I have no idea how to make the right input file. Can someone help me out with this? I have several MHC exon 2 sequences of several populations coming from different localities. Thank you very much to all.
Hi,
The input file for Arlequin requires a 'mantel' section to be added, e.g:
[[Mantel]]
MatrixSize= 5
MatrixNumber= 2
YMatrix= "fst"
YMatrixLabels = {
"Population1 " "Population2" "Population3"
"Population4" "Population5"
}
DistMatMantel={
0.00
3.50 0.00
0.87 0.32 0.00
0.07 1.76 1.65 0.00
0.28 0.98 0.27 0.47 0.00
}
UsedYMatrixLabels={
"Population1 "
"Population2"
"Population3"
"Population4"
"Population5"
}
Some notes:
MatrixSize corresponds to the number of populations used
A MatrixNumber of 2 means you're comparing two matrices i.e. genetic (e.g. Fst) and e.g. geographic (the values in DistMatMantel)
YMatrix= "fst" means Arlequin should use the Fst distance (other options are log_fst, slatkinlinearfst, log_slatkinlinearfst, nm, and custom (i.e. user supplied).
Hope that helps!
Hi,
The input file for Arlequin requires a 'mantel' section to be added, e.g:
[[Mantel]]
MatrixSize= 5
MatrixNumber= 2
YMatrix= "fst"
YMatrixLabels = {
"Population1 " "Population2" "Population3"
"Population4" "Population5"
}
DistMatMantel={
0.00
3.50 0.00
0.87 0.32 0.00
0.07 1.76 1.65 0.00
0.28 0.98 0.27 0.47 0.00
}
UsedYMatrixLabels={
"Population1 "
"Population2"
"Population3"
"Population4"
"Population5"
}
Some notes:
MatrixSize corresponds to the number of populations used
A MatrixNumber of 2 means you're comparing two matrices i.e. genetic (e.g. Fst) and e.g. geographic (the values in DistMatMantel)
YMatrix= "fst" means Arlequin should use the Fst distance (other options are log_fst, slatkinlinearfst, log_slatkinlinearfst, nm, and custom (i.e. user supplied).
Hope that helps!
You can perform this test on the software GENETIX it is very easy (looking for help)
or With this software you work directly on the Internet, you must go to Google: IBD Mantel test: IBD - San Diego State University has welcomes the page.
1- I click IBDWS (he cries and highlight in blue)
2- He leaves us a page is clicked: genetic distances / Similarities,
3- We have a page one can descend with the cursor and found (writing in blue) 1 INPUT DATA ------- ahead is looking for my file that I should have a .txt file and modify as next you find with the Software folder (Example of software IBD matrix that Mantel test), open,
4- I go to the next window 2 BASIC SETTINGS, I check all hawksbill including the latest,
5- I spend a 3 SUBMIT ---- I submit is the result, the null hypothesis here is that r = 0, if so I have a small P-value I reject H0 is saying that r is significantly different from 0 is that there is a correlation either positive or negative between the two dies following property on the door sign that the value of r.
I hoped to have help you
Dear Karneo Lst,
Angela McGaughran provided you with the piece of text you have to include in your arlequin project file (.arp) to perform the Mantel test.
To compute the geographic distance matrix for your populations, you can use the R package AFLPdat (A collection of R functions for handling AFLP data, Dorothée Ehrich, 2007). This package has one function called Geodist, that computes the geographic distance matrix. This function uses as input a tab-separated text file with three columns (the first one for the population names and the second and third ones for the latitudes and longitudes- expressed in Degrees with decimals).
You may download AFLPdat from here: http://www.nhm.uio.no/english/research/ncb/aflpdat/
I have 15 populations and I with seven groups. How can I make input for geographic distance fro Mantel test? please, suggest me.
Thanks
Rakeb
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