Torsten's opinion would be appreciated: Different tree topologies while using Gubbins and IQ-Tree

[alanxelena]

Dear @tseemann,

I'm running an SNP phylogeny as you suggested here: https://github.com/tseemann/snippy

My problem is that if I compare the nwk tree generated by gubbins and that from IQ-tree I get very different topologies and I can't find the explanation for this. I've had some exchange with nickjcroucher in this thread:

https://github.com/nickjcroucher/gubbins/issues/354

Do you have any opinions on which approach would be the right one?

Any comment would be greatly appreciated.

Alan.