Hi all,

I have some phylip files which I was able to generate using stacks pipeline. It contains SNPs which are fixed within populations. So there are lot of N's in the results. I found that it is possible to draw only Maximum likelihood trees from this data.

So I want to is it not possible to draw neighbor joining trees from NGS data using Stacks outputs. If there is a way please let me know.

Thank you in advance.

Regards,

kmkdesilva