Hi Kuldeep More ... Well, I believe it is far beyond the software's capacity, but you might workaround this by first, reducing your dataset for haplotypes only (not all samples), then variable sites only (conserved sites doesn't mater here). Given the size of your dataset, I recommend you to do that with some processing language like Perl, R, Python, or even in bash (in a fasta/vcf aligned file). If you are not familiar with, you might try regular softwares as DNAsp (v6 or higher), MEGA and others. You can still entering haplotypes' frequencies and locality data with "trait blocks/files" (see PopArt manual for details).

DNAsp seems an interesting choice because authors have optimized it to work with SNP data, so it should have the capacity to handle your data (but look at the manual first). Also, DNAsp has a specific module to generate haplotype files for network softwares, exporting data in nexus and other output formats, and generating haplotype frequencies files.

Good luck.

Cheers

Wilson