Maximum Likelihood Phylogeny for protein alignments produces sub-optimal trees for some substitution models
Issue description
When running Maximum Likelihood Phylogeny with a protein alignment as input, the resulting tree will not be the maximum likelihood tree if one of the following substitution models is selected:
Instead, the starting tree – either built from the provided alignment, or (optionally) supplied in the wizard – is provided as a result. This is likely to have different branch lengths and topology than the actual maximum likelihood tree.
Affected software
CLC software versions 24.0 and earlier that offer maximum likelihood analysis of protein data using the Dayhoff (PAM), JTT, and WAG substitution models are affected.
This problem was addressed in version 24.0.1.
