>>>> begin comments - do not remove this line <<<< Here is a description of the format. Any information is stored on two lines, the first for the type of information, the second for the content. === Lines starting with ">>" === They store generic information about the loci or the individuals. They are all optional. Character strings following the ">>" can match: - "position": the following line contains integers giving the position of the SNPs on the sequence - "allele": the following line contains a vector of two alleles separated by "/" - "population": population, or more generally a grouping factor for the individuals - "ploidy": the ploidy of each individual given as an integer; alternatively, one single integer if all individuals have the same ploidy - "chromosome": the chromosome where the SNP are located Elements are separated by a space, and their length must match exactly the number of loci (position, allele, chromosome) or individuals (population, ploidy). Therefore, no space is allowed for the names of these items (especially chromosomes or populations). === Lines starting with ">" === They store individual genotypes. The character string following the sign ">" is the label of the individual. Spaces before and after are ignored. The following line contains integers without separators, each representing the number of copies of the second allele. Missing values are to be coded by a single non-integer character (by default, "-"). For instance, in the following toy dataset: - foo ("1020") is "at" at position 1, "gg" at position 8, "cc" at position 11, and "tt" at position 43. - bar ("0012") is "aa", "gg", "ac" and "aa" - toto ("10-0") is "at", "gg", not typed (NA) and "tt" >>>> end comments - do not remove this line <<<< >> position 1 8 11 43 >> allele a/t g/c a/c t/a >> population Brit Brit Fren monster NA >> ploidy 2 > foo 1020 > bar 0012 > toto 10-0 > Nyarlathotep 0120 > an even longer label but OK since on a single line 1100