What is the role of reading frames in GARLI codon analysis?
One thing to note is that codon models for tree inference require that you align the protein coding sequences along a correct reading frame; (e.g., gaps of 1 or 2 bases will impair the analysis). Maintaining the reading frame makes alignment much easier even if your analysis will be at the nucleotide level. Just running sequences through a sequence alignment program without looking is almost guaranteed to return an alignment that will not work for codon based inference.
