Is baseml (PAML) suitable for ancestral reconstruction of non-coding sequences?

Question

[memory_donk]

Hi Biostars,

I'm not super familiar with the underlying data used to general substitution models or how programs like PAML utilise them for ancestral reconstructions. I'm hoping though, to do ancestral reconstructions of several non-coding (putative enhancer) sequences and wasn't sure whether PAML's substitution models are only geared toward protein-coding sequences (which would probably look quite different in terms of substitution patterns). If anyone knows which models would be best for this purpose (if any in PAML) or a program that would be more appropriate I'd greatly appreciate it.