Supporting Modified Alphabets

[k-forghani]

Dear developers,
Can VeryFastTree handle a modified alphabet rather than either nucleotide or amino acid alphabets?
If yes, how can it be performed?
Thanks in advance.

[cesarpomar]

VeryFastTree is built upon the algorithms of FastTree, designed for protein and nucleotide sequences. Introducing a new alphabet would indeed necessitate significant changes, depending on the nature of the modifications you have in mind. Nevertheless, if you have a proposal for such a modification, we are open to discussing its feasibility and potential implementation. Please provide more details on the specific modifications you're considering, and we can explore the possibilities further.