Hello all, I set up an analysis with Mr bayes with a DNA partition and an indel-partition (binary) I obtained from Fastgap. I set MrBayes as suggeted in the manual (here example):

Format datatype=mixed(dna:1-1000,restriction:1001-1200)

and for the Indel-partition:

lset app=(2) coding=variable rates=gamma

2 questions:

a) How do I set the statefreqpr for the indel-partiton right? I used statefreqpr=fixed(equal)

b) Should I set ratepr=variable when I use indel-partitions mixed with DNA partitiond (these contain non-coding and sometimes also protein-coding (codon) regions)

Thanks for your help All the best Dieter