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

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

## MODELS OF EVOLUTION: all | allx | mrbayes | beast | gamma | gammai | <list> ##
models = HKY, GTR, GTR+G, GTR+I+G;

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

## DATA BLOCKS: see manual for how to define ##
[data_blocks]
coding = 3964-4920\3;5132-6181\3;6588-8132\3;8275-8958\3;9032-10658\3;10728-11075\3;11145-12814\3;13015-15346\3;15425-16564\3;
non-coding = 6254-6271;8201-8204;8959-8961;15416-15424;
tRNA = 1178-3963;4921-5131;6182-6253;6272-6418;6451-6587;8133-8274;8962-9031;10659-10727;11076-11144;12815-13014;15347-15415;16565-16702;
D-loop = 1-1177;6419-6450;16703-17618;

## SCHEMES, search: greedy | user | greedy | rcluster | rclusterf | kmeans ## 
[schemes]
search = greedy;