Settings used alignment : ./Mylo_7exons_seqCat.phylip branchlengths : linked models : GTR+I+G, GTR+G model_selection : bic search : greedy Best partitioning scheme Scheme Name : step_12 Scheme lnL : -61830.71542 Scheme BIC : 125038.535538 Number of params : 143 Number of sites : 15216 Number of subsets : 9 Subset | Best Model | Subset Partitions | Subset Sites | Alignment 1 | GTR+G | ADORA3_pos1, ADORA3_pos2, APOB_pos2 | 1-312\3, 2-312\3, 314-2724\3 | ./analysis/phylofiles/395423563a2cf015f7b26e0541dab606.phy 2 | GTR+G | ADORA3_pos3, APOB_pos3, RAG2_pos3 | 3-312\3, 315-2724\3, 10374-10797\3 | ./analysis/phylofiles/257eca5e33c48a87f0d7cc16eb3182d0.phy 3 | GTR+G | APOB_pos1, BRCA1_pos1 | 313-2724\3, 3706-6483\3 | ./analysis/phylofiles/64ca94274bad53c25431b07c2db1f54d.phy 4 | GTR+G | BCHE_pos1, RAG2_pos1, TTN_pos1 | 2725-3705\3, 10372-10797\3, 10798-15216\3 | ./analysis/phylofiles/f02368c5a1e593374be4361dab572cd2.phy 5 | GTR+I+G | BCHE_pos2, RAG2_pos2, TTN_pos2 | 2726-3705\3, 10373-10797\3, 10799-15216\3 | ./analysis/phylofiles/44fb797f8d2b0606cc3f16d245722845.phy 6 | GTR+G | BCHE_pos3, BRCA2_pos3 | 2727-3705\3, 6486-10371\3 | ./analysis/phylofiles/53339eae8fe848930d90d326ac73030c.phy 7 | GTR+G | BRCA1_pos2, BRCA2_pos2 | 3707-6483\3, 6485-10371\3 | ./analysis/phylofiles/e18b4cf871640e942b5f1b3613bfb5a7.phy 8 | GTR+G | BRCA1_pos3, TTN_pos3 | 3708-6483\3, 10800-15216\3 | ./analysis/phylofiles/99418eb75b3659a9b61f9459d93c131b.phy 9 | GTR+G | BRCA2_pos1 | 6484-10371\3 | ./analysis/phylofiles/fa88e61dbe34f2b3de0f18107290ea9c.phy Scheme Description in PartitionFinder format Scheme_step_12 = (ADORA3_pos1, ADORA3_pos2, APOB_pos2) (ADORA3_pos3, APOB_pos3, RAG2_pos3) (APOB_pos1, BRCA1_pos1) (BCHE_pos1, RAG2_pos1, TTN_pos1) (BCHE_pos2, RAG2_pos2, TTN_pos2) (BCHE_pos3, BRCA2_pos3) (BRCA1_pos2, BRCA2_pos2) (BRCA1_pos3, TTN_pos3) (BRCA2_pos1); RaxML-style partition definitions DNA, p1 = 1-312\3, 2-312\3, 314-2724\3 DNA, p2 = 3-312\3, 315-2724\3, 10374-10797\3 DNA, p3 = 313-2724\3, 3706-6483\3 DNA, p4 = 2725-3705\3, 10372-10797\3, 10798-15216\3 DNA, p5 = 2726-3705\3, 10373-10797\3, 10799-15216\3 DNA, p6 = 2727-3705\3, 6486-10371\3 DNA, p7 = 3707-6483\3, 6485-10371\3 DNA, p8 = 3708-6483\3, 10800-15216\3 DNA, p9 = 6484-10371\3