Hello everyone,
I am fairly new to using BAPs, and I need some help. I have 140 sequences of the same gene, same species. I am trying to determine if there is structure from 5 sampled populations. My questions are:
1) is this possible in BAPs? Or is there another program that would better fit my needs?
2) how would I go about formatting the input file to include my groupings? I could only get the input file to work in a .xls format.
I have read through the manual, and I'm sure I have overly confused myself. Any and all help is greatly appreciated. Thank you!!
Hi Savannah,
There are many statistical procedures besides BAPS that are generaly used to infer population structure but I would suggest first to seek for sign of phylogeographic structure within your data (relationship between haplotypes and their geographic origin) by using PERMUT; if you found significant difference between Nst and Gst (Nst significantly larger than Gst), then your data support the existence of phylogeographic structure. On the other hand, you can still run SAMOVA if you notice a particular divergence among samples based on haplotype network or genetic distance matrix. Running MDS (multidimensional scaling) on genetic distances would make the task more easier and allow revealing particuar population grouping. AMOVA implemented in Arlequin would also be useful to test for population structure under different biogeographic hypotheses and based on the outcome of your MDS and network analyses.
BAPS versions 5 and 6 are now able to infer population structure based on DNA sequences. BAPS is generally used for clustering the sampled haplotypes into monophyletic clusters of haplotypes (haplogroups). You should decide about the maximum number of clusters (K) according to your data. Haplotypes would be then assigned to one of the clusters by admixture analysis.
I advise you to follow and format the input file (example dedicated for sequence data) found in the BAPS package, according to your data. This would be much more easier and would save time also!
I hope this would help, Good luck!
Dear Savannah,
I used BAPS to detect genetic structure in many of my mtDNA sequence datasets. I think it is an excellent software.
You need to construct 4 input .txt files: data, pops, index and nums. "data.txt" includes your rough sequences plus a progressive number at the end of each sequence (sequence lengths should be equal); "pops.txt" includes the name of your populations plus a blank and progressive number at the end; "index.txt" includes a column of numbers each indicating the first individual of each population; and "nums.txt" in your case is a simple series of number (from 1 to No. of bp) separated by blanks. After you launch BAPS, you have to click on "Clustering with linked loci" and follow the steps. Note that it is important to replicate each k-value. I usually use 5 replicates for each k-value. You have just to type "2 2 2 2 2 3 3 3 3 3 .... No. of pops +3" when the program asks it. At the end, the program produces a file .mat. Use it as input for the successive analysis ("Admixture based on mixture clustering"). At the end you'll obtain another .mat file with results. I usually edit results with Excel, in order to obtain assignment graphs. That's it.
If you need further details, do not hesitate to contact me.
ciao
f.m.
Hello
I'm fairly new to using BAP, and I need help.
I have SSR data from populations of the same species. I am trying to determine if there is a structure of 14 populations sampled.
My question is: How will I format the input file?
Thank you very much
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