Dear all, We posted a couple of questions about using Arlequin to analyze sequence data from nuclear genes a few days ago. Many folks sent me several nice ideas and many others asked to know the answers I got. I figured it would be easier to just post what I thought was most significant: Here is what I previously posted: >Some information about the data: >-the data comes from direct sequencing of PCR fragments of a nuclear >gene, from a diploid species. Therefore, the heterozygotes for a SNP apear >with the degenerate code (R, Y, etc). > >-We build the input with the different haplotypes found in each population >The problem: >-we cannot get the program to interpret the degenerate code. The way things are >going now, it dismisses any SNP position with a degenerate code and therefore interprets all the >haplotypes as being the same. The solutions/answers: -even though the manual says so, arlequin does not interpret sequence degenerate codes, at least for the type of data we have (diploid, unknown phase) -there are two basic ways to deal with the situation: (1) one can convert the sequence data into genotypes at the variable sites/SNPs and analize the data that way, as genotypic data, phase unknown. (2) there are ways to predict haplotypes from this type of data, which can then be inputed into arlequin, and other programs, as phase known haplotypes, etc. See Kidd et al. 2000 Am. J. Hum. Gen. Many thanks to all of you who tried to help us! cheers, alex Alexandre Rodrigues Caetano, Ph.D. Embrapa Recursos Genéticos e Biotecnologia Parque Estação Biológica Final Av. W/5 Norte, Brasília-DF C.P. 02372 70770-900 Brasil Tel.: (55)-61-448-4778 Fax: (55)-61-340-3658 acaetano@cenargen.embrapa.br http://www.cenargen.embrapa.br/ "Alexandre R. Caetano"