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
Has any sense run a bootstrapping when using CLustal Omega?
Is there aby boostrapping program that uses the same algorithm that CLustal Omega
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