The FASTA files (unpacked) in the subdirectory "data" of the PopGenome package have to be stored in a folder (multiple files can be stored in this folder). The folder name is then used as the input for the readData function.
A typical GFF file which should be stored in a folder (for example in "GFF"). This folder is the input for the readData(...,gffpath="GFF") function. The corresponding FASTA file is stored in the "data" subdirectory of the PopGenome package. It has to be stored in a folder with the SAME NAME as the GFF file (for example in "FASTA"). readData("FASTA", gffpath="GFF")
A VCF file stored in the directory "data" of the PopGenome package. The file (unpacked) has to be stored in a folder (for example "VCF"). Note that many VCF-files can be stored in this folder and are read consecutively. If the VCF file is too large to fit into the computer's main memory, split it into chunks (by position) ! PopGenome is able to concatenate these chunks afterwards. readData("VCF",format="VCF",FAST=TRUE)
snp_file
(Package: PopGenome) :
.SNP file (variant call data from 1001 Arabidopsis Genomes project)
A .SNP file stored in the directory "data" of the PopGenome package. The file contains variant calls for exactly one individual. Put all files (individuals of interest) into one folder (for example "SNP"). readSNP("SNP",CHR=1)
providing 
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