strange results tree

[pavlo888]

dear,

I have successfully managed to apply gotree to a set of >200 bacterial genomes. However, the results I have obtained are incongruent to those I obtained with a multiple-locus sequence analysis. I was wondering if you could help me find an explanation for this occurrence? My main issue is that the similarity distances (branch distances) between clusters are too short. Do you have any idea of what a good similarity threshold is advisable for this kind of output, e.g. 97% similarity?

Cheers,
Pablo