neighbor joining tree

I am doing unifrac analysis on my data
For this i did following steps

  1. calculated distance
  2. generated tree
  3. unifrac
    unifrac.unweighted(tree=test.phylip.tre, group=test.groups)
  4. Did PCoA

I have used neighbor joining method in clearcut command to generate tree but its still generating phylip tree. Is there huge difference in downstream analysis based on phylip or neighbour joining?
Also how can i generate neighbour joining tree both for phylo.diversity and unifrac analysis?

looking forward for your reply

Thank you in advance

It’s the same thing - both are outputted in newick format.