Bootstrap values in Gubbins final tree

Question

[lizabe]

Hi! I am generating a phylogenetic tree using Gubbins, The problem is that I finally have only the branch lengths onto the final tree. Any idea what I'm doing wrong?

Thanks in advance!

Answer 1

[Brice Sarver]

I haven't used that application, but I don't see anything in the documentation about bootstrap resampling being used to generate nodal support values. You're probably getting a point estimate of the tree out with just the branch lengths (as you'd expect). Perhaps you could use this tree, fix the topology, and estimate bootstrap support values using another approach (e.g., RAxML, PAUP*)? RAxML may be able to do this with a dataset of your size, assuming you're using Grubbins because you have a lot of data and the calculations are rate-limiting, but maybe not.