Hi all,

I want to perform analysis of ancient population history using Stairway Plot.

Manual told me, that as input file I should prepare SFS file, consisting some information concerning SNP:

"... Input file format:

Columns are separated by TABs.

Second row: nseq-1 columns, each is a count of the SNPs of a given size (i.e. \xi). All counts need to be provided, even though some of them will not be used for \theta estimation.

1st col: count of the SNPs of size 1 (i.e. \xi_1)

2nd col: count of the SNPs of size 2 (i.e. \xi_2)

...

nseq-1_th col: count of the SNPs of size nseq-1 (i.e. \xi_(nseq-1)) ..."

Can anybody knows, how can I create such file for my data in fasta format?

Also, any suggestion for other software for inferring population histories in the form of stairway plot are welcome.

Thanks in advance,

Danila