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brannala / BA3

BA3 is a software package for estimating rates of migration between populations using multilocus genotype data.
GNU Affero General Public License v3.0
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Using RADseq haplotype data #10

Open dorseyb opened 7 months ago

dorseyb commented 7 months ago

Hello Dr. Rannala,

Is there any reason I should not use the haplotypes of RADseq loci in BA3SNP as long as I filter for <= 4 alleles/locus? It seems that they would be treated the same by the program. I can choose a random snps from each locus, but there is more information in the haplotype data so I would like to use that set.

Thanks for any advice.

Cheers, Brian D.

brannala commented 7 months ago

Hi Brian, The model in BA3 is based on genotype data; it essentially treats loci as independently assorting so that haplotypes provide no additional information. This assumption (independent assortment) was reasonable in the early 2000s when the program was first developed and the data were typically microsatellites with only a few dozen loci available at unknown positions in the genome. In order to use haplotype information an explicit model of linkage and recombination is needed as well as a linkage map. When thousands of loci are used the current BA3 program is essentially a composite likelihood method. I may implement such features in a future version but with the current version you will have to provide the data as genotypes.