Settings used

alignment         : ./2cpDNA.phy
branchlengths     : unlinked
models            : JC, K80, SYM, F81, HKY, GTR, JC+G, K80+G, SYM+G, F81+G, HKY+G, GTR+G, JC+I, K80+I, SYM+I, F81+I, HKY+I, GTR+I, JC+I+G, K80+I+G, SYM+I+G, F81+I+G, HKY+I+G, GTR+I+G
model_selection   : aicc
search            : greedy


Best partitioning scheme

Scheme Name       : step_7
Scheme lnL        : -5773.5205078125
Scheme AICc       : 12110.0614238
Number of params  : 253
Number of sites   : 2508
Number of subsets : 1

Subset | Best Model | # sites    | subset id                        | Partition names                                                                                     
1      | GTR+I+G    | 2508       | 29463fa4f6c11558af9cd688ebb0ac65 | matK_pos1, matK_pos2, matK_pos3, rpl32_pos2, rpl32_pos3, rpl32_pos1, interspacerrpl, tranK          


Scheme Description in PartitionFinder format
Scheme_step_7 = (matK_pos1, matK_pos2, matK_pos3, rpl32_pos2, rpl32_pos3, rpl32_pos1, interspacerrpl, tranK);

Nexus formatted character sets
begin sets;
	charset Subset1 = 1-1443\3 2-1443\3 3-1443\3 1444-1610\3 1445-1610\3 1446-1610\3 1611-2484 2485-2508;
	charpartition PartitionFinder = Group1:Subset1;
end;


Scheme Name       : start_scheme
Scheme lnL        : -5536.505073547363
Scheme AICc       : 30147.2630207
Number of params  : 1985
Number of sites   : 2508
Number of subsets : 8

Subset | Best Model | # sites    | subset id                        | Partition names                                                                                     
1      | GTR+I+G    | 481        | cbfcbb9dd346bb65dce73cc957eb02f1 | matK_pos1                                                                                           
2      | F81+I      | 481        | 43387d1bc495974dd957e56ecfd13d3e | matK_pos2                                                                                           
3      | GTR+G      | 481        | ec91d759a9a95926b169a28133023137 | matK_pos3                                                                                           
4      | JC         | 56         | 7bc74eedb5b4135760d97f0818c7db24 | rpl32_pos2                                                                                          
5      | HKY+I+G    | 56         | f1170c466f24f466f1e98246c4727e85 | rpl32_pos3                                                                                          
6      | F81        | 55         | 769c5b90330d32018c81b6d321b93b7e | rpl32_pos1                                                                                          
7      | GTR+G      | 874        | 7c8e439891156c7905cd16bc2fc2a676 | interspacerrpl                                                                                      
8      | JC         | 24         | 78c013cfafcaa6972d1c835b46afced1 | tranK                                                                                               


begin mrbayes;

	charset Subset1 = 1-1443\3;
	charset Subset2 = 2-1443\3;
	charset Subset3 = 3-1443\3;
	charset Subset4 = 1444-1610\3;
	charset Subset5 = 1445-1610\3;
	charset Subset6 = 1446-1610\3;
	charset Subset7 = 1611-2484;
	charset Subset8 = 2485-2508;

	partition PartitionFinder = 8:Subset1, Subset2, Subset3, Subset4, Subset5, Subset6, Subset7, Subset8;
	set partition=PartitionFinder;

	lset applyto=(1) nst=6 rates=invgamma;
	lset applyto=(2) nst=1 rates=propinv;
	lset applyto=(3) nst=6 rates=gamma;
	lset applyto=(4) nst=1;
prset applyto=(4) statefreqpr=fixed(equal);
	lset applyto=(5) nst=2 rates=invgamma;
	lset applyto=(6) nst=1;
	lset applyto=(7) nst=6 rates=gamma;
	lset applyto=(8) nst=1;
prset applyto=(8) statefreqpr=fixed(equal);

	prset applyto=(all) ratepr=variable;
	unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all) tratio=(all);
	unlink brlens=(all);

end;