## ALIGNMENT FILE ## alignment = infile.phy; ## BRANCHLENGTHS: linked | unlinked ## branchlengths = linked; ## MODELS OF EVOLUTION: all | allx | mrbayes | beast | gamma | gammai | ## models = mrbayes; # MODEL SELECCTION: AIC | AICc | BIC # model_selection = bic; ## DATA BLOCKS: see manual for how to define ## [data_blocks] tRNA-Phe = 1-54; 12S_rRNA = 55-933; tRNA-Val = 934-995; 16S_rRNA = 996-2371; tRNA-Leu_1 = 2372-2447; ND1_C1 = 2448-3088\2; ND1_C2 = 2449-3088\2; tRNA-Ile = 3089-3160; tRNA-Gln = 3161-3230; tRNA-Met = 3231-3299; ND2_C1 = 3300-3993\2; ND2_C2 = 3301-3993\2; tRNA-Trp = 3994-4064; tRNA-Ala = 4065-4133; tRNA-Asn = 4134-4209; tRNA-Cys = 4210-4276; tRNA-Tyr = 4277-4346; COX1_C1 = 4347-5378\2; COX1_C2 = 4348-5378\2; tRNA-Ser_1 = 5379-5455; tRNA-Asp = 5456-5527; COX2_C1 = 5528-5982\2; COX2_C2 = 5529-5982\2; tRNA-Lys = 5983-6055; ATP8_C1 = 6056-6171\2; ATP8_C2 = 6057-6171\2; ATP6_C1 = 6172-6621\2; ATP6_C2 = 6173-6621\2; COX3_C1 = 6622-7143\2; COX3_C2 = 6623-7143\2; tRNA-Gly = 7144-7215; ND3_C1 = 7216-7449\2; ND3_C2 = 7217-7449\2; tRNA-Arg = 7450-7519; ND4L_C1 = 7520-7715\2; ND4L_C2 = 7521-7715\2; ND4_C1 = 7716-8625\2; ND4_C2 = 7717-8625\2; tRNA-His = 8626-8697; tRNA-Ser_2 = 8698-8764; tRNA-Leu_2 = 8765-8835; ND5_C1 = 8836-10035\2; ND5_C2 = 8837-10035\2; CytB_C1 = 10036-10799\2; CytB_C2 = 10037-10799\2; tRNA-Thr = 10800-10870; tRNA-Pro = 10871-10943; NADH6_C1 = 10944-11291\2; NADH6_C2 = 10945-11291\2; tRNA-Glu = 11292-11362; 3CODONRY = 11363-15138; ## SCHEMES, search: all | user | greedy | rcluster | rclusterf | kmeans ## [schemes] search = greedy;