## ALIGNMENT FILE ##
alignment =infile.phy;

## BRANCHLENGTHS: linked | unlinked ##
branchlengths = linked;

## MODELS OF EVOLUTION: all | allx | mrbayes | beast | gamma | gammai | <list> ##
models = all;

# MODEL SELECCTION: AIC | AICc | BIC #
model_selection = BIC;

## DATA BLOCKS: see manual for how to define ##
[data_blocks]
atp6  =   1-230;
atp8  =   231-292;
cob   =   293-671;
cox1  =   672-1191;
cox2  =   1192-1429;
cox3  =   1430-1689;
nad1 =   1690-2006;
nad2 =   2007-2350;
nad3 =   2351-2468;
nad4 =   2469-2940;
nad4l =  2931-3024;
nad5 =  3025-3626;
nad6 =   3627-3791;
## SCHEMES, search: all | user | greedy | rcluster | rclusterf | kmeans ##
[schemes]
search = user;
together = (atp6, atp8, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4l, nad5, nad6);

separate = (atp6) (atp8) (cob) (cox1) (cox2) (cox3) (nad1) (nad2) (nad3) (nad4) (nad4l) (nad5) (nad6);

subunit = (atp6, atp8) (cob) (cox1, cox2, cox3) (nad1, nad2, nad3, nad4, nad4l, nad5, nad6);