## ALIGNMENT FILE ##
alignment = cats_mt_feb8.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]

D-loop = 1-1177\1; 6419-6450\1; 16703-17618\1;
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\1; 8201-8204\1; 8959-8961\1; 15416-15424\1;
tRNA = 1178-3963\3; 4921-5131\3; 6182-6253\3; 6272-6418\3; 6451-6587\3; 8133-8274\3; 8962-9031\3; 10659-10727\3; 11076-11144\3; 12815-13014\3; 15347-15415\3; 16565-16702\3;


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