Hello, by any chance does someone here have experience working with PAUP and could help me with my question? I would be really grateful. I need to do a phylogeny analysis by concatenating 5 genes, but for each one I need to use a different nucleotide substitution model. I am using a file in nexus format, with the syntax of the image, and the program does run, but I do not know if it is really following the instructions that I gave it. I have already looked in the manual and internet, I know that an analysis can be done by partition, but I cannot find how to define each model for each charset. It is an analysis using maximum likelihood. Thank you very much in advance.

I am using this:

begin sets;

charset gene1 = 1- 267;

charset gene2 = 268- 792;

charset gene3 = 793- 1276;

charset gene4 = 1277- 1708;

charset gene5= 1709- 2200;

charpartition genes = 1:1-267, 2:268-792, 3:793-1276, 4:1277-1708, 5:1709-2200;

end;

begin paup;

Lset Base=equal Nst=6 Rmat=(0.0001 1.1918 0.5104 0.0001 1.1918) Rates=equal Pinvar=0.8209;

Lset Base=(0.2209 0.3018 0.2372) Nst=2 TRatio=1.7800 Rates=equal Pinvar=0.7088;

Lset Base=(0.2177 0.3085 0.2276) Nst=6 Rmat=(1.0000 6.8574 2.2215 2.2215 6.8574) Rates=equal Pinvar=0;

Lset Base=(0.2293 0.3876 0.1950) Nst=6 Rmat=(0.0001 5.7243 2.4396 0.1357 5.7243) Rates=gamma Shape=0.1117 Pinvar=0;

Lset Base=(0.2224 0.3270 0.2016) Nst=2 TRatio=1.7040 Rates=equal Pinvar=0.7502;

end;