The problem is as follows: I got VCF file obtained by GATK for 288 individuals, then I convert it to nucleotide fasta (using PGDSpider) so the length of individual's fasta sequence corresponds to the number of SNPs in VCF file. If I want to use MEGA to build a tree I first make an alignment which adds gaps that are actually are not in favor in that case. So the question is how to make an alignment file (*.meg) without gaps in order to make a tree in MEGA?
Question: How to build a phylogenetic tree using fasta obtained from VCF file?
20 months ago by
rimgubaev • 190
rimgubaev • 190 wrote:
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