asterisk in phylip file

Question

[Chenfei Zheng]

Dear all: There were so many asterisk (*) in my output phylip sequences when I converted a vcf file into phylip format using vcf2phylip. Can anybody help solve this problem? Thank you

[liorglic]

Please provide a sample from your file so we can understand what you are talking about.

[Chenfei Zheng]

Answer 1

[Klaus S]

It looks like "*" represents a gap "-".

[Chenfei Zheng]

Thank you for your reply. This "" can not be identified by following programs like iqtree. I've tried to remove those snp positions in vcf file, but new "" always arise after old ones were deleted. Do you know how to fix this? Thank you.