Generate a MAP file from a fasta file

Question

[ddeliadoreen]

Hi to all,

I have a fasta file having SNPs sequences that I extracted from a concatenate of five fragments of different genomic region (I am working on Anopheles funestus mosquito sequences). I would like to get MAP and PED files to plot a Linkage disequilibrium map in Haploview. I have been trying to get those files in PGDSpider and a was able to generate the PED file, while for the MAP file I am getting an error message 'map file cannot be created as there is no loci information'. I just wonder if I did properly filled my fasta file header or if there is any other program that i can use to get these files.

Thanks in advance,

Delia.