I converted vcf file to fasta file, then I used Treebest to build NJ tree with command " treebest nj -W -t ntmm -b 1000 fastfile > result", Error occurred:
[ma_trans_align] not seem to be a nucleotide alignment (218638).
[ma_nucl_filter] fail to translate a nucleotide alignment. Filtering abort.
I couldn't find what was wrong.