Hi Rob, may I ask an additional question on this very topic, once is still about the same analysis.
Could you check if these blocks are determined in the right way? I mean, in an alignment of 3 genes, I want to test which partition scheme is better:
-everything as a single block (one single or no partition)
-separate the third codon position from the rest (1+2)
-separate each gene (including the third position of each gene)
-separate each gene and each third codon position (max number of partitions)
I deliberately not assumed a partition between 1st and 2nd position both because my alignment is quite big and because there seems not to have variation even among the third codon positions, and this is the very reason for my question: please, could you check if my configuration of those schemes are right, because the results from PF has been always the first one (everything as a single partition). I'm using the BIC as a reference.
Here are the specific lines from the .cfg file:
charset gene1 = 1-2973\3;
charset gene2 = 2974-4349\3;
charset gene3 = 4350-5949\3;
charset gene1_3 = 3-2973\3;
charset gene2_3 = 2976-4349\3;
charset gene3_3 = 4352-5949\3;
## SCHEMES ##
allsame123 = (gene1, gene2, gene3, gene1_3, gene2_3, gene3_3);
allsame_3 = (gene1, gene2, gene3) (gene1_3, gene2_3, gene3_3);
each_gene123 = (gene1, gene1_3) (gene2, gene2_3) (gene3, gene3_3);
each_gene12_3 = (gene1) (gene2) (gene3) (gene1_3) (gene2_3) (gene3_3);
Thanks a million for this,
bests,
Alex
On Monday, October 22, 2012 3:40:41 PM UTC-2, Alexandre wrote: