Settings used

alignment         : ./Untitled.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_6
Scheme lnL        : -9632.7294921875
Scheme AICc       : 19860.608486
Number of params  : 260
Number of sites   : 2067
Number of subsets : 1

Subset | Best Model | # sites    | subset id                        | Partition names                                                                                     
1      | SYM+I+G    | 2067       | cdb39a4fe4122461edcc81ac149cc123 | ETS1, 18s1, 18S2, ITS1, 5S, ITS2, 26S                                                               


begin mrbayes;

	charset Subset1 = 1-1111 1112-1139 1140-1410 1411-1639 1640-1803 1804-2021 2022-2067;

	partition PartitionFinder = 1:Subset1;
	set partition=PartitionFinder;

	lset applyto=(1) nst=6 rates=invgamma;
prset applyto=(1) statefreqpr=fixed(equal);

end;


Scheme Name       : start_scheme
Scheme lnL        : -9176.431293487549
Scheme AICc       : 45389.8260906
Number of params  : 1792
Number of sites   : 2067
Number of subsets : 7

Subset | Best Model | # sites    | subset id                        | Partition names                                                                                     
1      | SYM+G      | 1111       | 17e3c13193466f47de897e532eab5429 | ETS1                                                                                                
2      | JC         | 28         | 0786a1da9d75b2ef6e8d4f7dc595d8d9 | 18s1                                                                                                
3      | JC         | 271        | f85a1f7f239d72b84bea469ad78faed8 | 18S2                                                                                                
4      | SYM+G      | 229        | 34f09c6f47d779691733b7f2d6749bb0 | ITS1                                                                                                
5      | K80+I      | 164        | df823079fc2317dd30ec5d7903b5788b | 5S                                                                                                  
6      | SYM+G      | 218        | ff4237e0cdb49cfa080ed2e20caa09b4 | ITS2                                                                                                
7      | JC+I       | 46         | f0421ca86e479dba1bc5552fd0e87b13 | 26S 


begin mrbayes;

	charset Subset1 = 1-1111;
	charset Subset2 = 1112-1139;
	charset Subset3 = 1140-1410;
	charset Subset4 = 1411-1639;
	charset Subset5 = 1640-1803;
	charset Subset6 = 1804-2021;
	charset Subset7 = 2022-2067;

	partition PartitionFinder = 7:Subset1, Subset2, Subset3, Subset4, Subset5, Subset6, Subset7;
	set partition=PartitionFinder;

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

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

end;