The partitions and models of DNA sequences are like that:
DNA, coi_3 = 1 - 649\3;
DNA, coi_1 = 2 - 650\3;
DNA, coi_2 = 3 - 651\3;
DNA, h3_3 = 652 - 994\3;
DNA, h3_1 = 653 - 995\3;
DNA, h3_2 = 654 - 996\3;
DNA, 12s = 997 - 1352;
DNA, 16s = 1353 - 1805;
DNA, 28s = 1806 - 2686;
partition currentPartition = 9: coi_3, coi_1, coi_2, h3_3, h3_1, h3_2, 12s, 16s, 28s;
set partition = currentPartition;
lset applyto=(1, 2, 7, 9) nst=6 rates=gamma;
lset applyto=(4) nst=2 rates=gamma;
lset applyto=(6) nst=2;
lset applyto=(3) nst=6 rates=propinv;
lset applyto=(5) nst=6;
lset applyto=(8) nst=6 rates=invgamma;
How should I assign these partitioned models for running RAxML-HPC BlackBox? If anyone know, please help me figure this out.
THANK YOU!
Fan Li