How do I downweight third position transitions only in a parsimony analysis?
First you need to identify the codon positions. Probably the most efficient way to do this is to set up a codons block where the reading frame for the coding genes is identified. Then you need to define the weighting for transitions and transversions by creating a step matrix within an assumptions block. Finally, use the ctype command within a paup block to apply the stepmatrix to 3rd position sites only. begin assumptions; charset coding = 2-457 660-896; charset noncoding = 1 458-659 897-898; charset 1stpos = 2-457\3 660-896\3; charset 2ndpos = 3-457\3 661-896\3; charset 3rdpos = 4-457\3 662-.
