You can read information about Clustal Omefa from the authors of this program to which I sent a message claiming some information. From this message you can get the idea that Clustal Omega does not provide you with a truly phylogenetical alignment. If you need an phylogenetical alignment, I recommend to use another program like ClustalW, Muscle, Cofee, etc. To get the phylogenetical distances, you need to run bootstrapping, and you can do it using IQ-tree, for example
Clustal Omega is only a multiple sequence alignment program. It is not a phylogenetic program. Consequently there is no
bootstrapping in Clustal Omega.
We do use trees in Clustal Omega, but they are guide-trees, I repeat, not phylogenetic trees. Guide-trees are used to define
the order in which pair-wise alignments are performed.
The pair-wise alignments are done in Clustal Omega using HMMs.
The clustering in Clustal Omega (in default mode) is achieved by I am not aware of any program that uses exactly the same
clustering approach as Clustal Omega.
My suggestion is to use Clustal Omega to produce a multiple sequence alignment and then use any suitable program to
estimate a phylogentic tree. ClustalW has the capability to estimate a phylogenetic tree and calculate bootstrap values.
Hope that helps.
Best wishes,
Fabian.
