Clustal Omega and bootstrapping

Question

[Antonio R. Franco]

I run Clustal Omega to get a cladogram

Clustal Omega uses a HMM algorithm to cluster sequences together

By the other hand, there are many programs to run bootstrapping with the alignments. One os such is IQ-Tree, which is fast, sensitive, and available locally or through a WEB server

However, I don't get the point.

How can you do a bootstrapping if the clustering method you used (HMM in Clustal) is not the same that the bootstrapping program uses?. I don't see that choice in the Iq-tree program

So I make the following questions

1. Has any sense run a bootstrapping when using CLustal Omega?

2. Is there aby boostrapping program that uses the same algorithm that CLustal Omega

3. What is more important. Is the HMM method sensitive and accurate enough to avoid the using of bootstraping

I know from the authors of Clustal Omega, that no bootstrapping is included in their algorithm

[Joe]

Are you talking about the guide tree that Clustal uses for the MSAs?

That's not the same as a proper phylogenetic tree, so it wouldn't be right to use that tree with any other phylogenetics tools, as far as I'm aware.