Is it possible to divide the data into partitions and assign different site models to each partition?
Yes,you can. Take a look at these tutorial http://beast.bio.ed.ac.uk/Tutorial_8 http://beast.bio.ed.ac.uk/Tutorial_6 The differences between these two tutorial: Tutorial 8: The different genes(locus) have different alignments. For example, the alignment for gene1 are “alignment1”, the alignment for gene2 are “alignment2”, the alignment for gene3 are “alignment3”; I think according to this tutorial, the different alignments of genes(locus) can have different taxons. For example, the “alignment1” have taxon A,taxon B,taxon C,taxon D; the “alignment2” have taxon A,taxon B,taxon C,taxon E; the “alignment3” have taxon A,taxon B,taxon C,taxon D, taxon E.
