Extract SNPs from alignments

A light-weight tool that extracts single nucleotide polymorphisms (SNPs) from FASTA alignments and saves them to a plink binary-format BED file. It is fast and can process whole-genome data on a laptop in minutes. The FASTA alignments should be in the format provided by the Drosophila Genome Nexus, i.e. the data for each line (or individual) are in a separate file with nucleotides in one line and without the customary FASTA header. Each chromosome arm has its own set of files.