dear, i have a simple dub to continue my next analysis:
I running PartionFinder via cipres with this partition having account the three codon position to Protein Coding Genes
model_selection = BIC;
ATP6_pos1 = 2035-2700\3;
ATP6_pos2 = 2036-2700\3;
ATP6_pos3 = 2037-2700\3;
ATP8_pos1 = 2701-2868\3;
ATP8_pos2 = 2702-2868\3;
ATP8_pos3 = 2703-2868\3;
COI_pos1 = 2869-4407\3;
COI_pos2 = 2870-4407\3;
COI_pos3 = 2871-4407\3;
etc.....
search = greedy;
In the results of Partition finder (I have 9subsets):
Subset | Best Model | # sites | subset id | Partition names
1 | GTR+I+G | 2200 | 2efec876c005c0b57996d5316ad54310 | 12S, ND1_pos1, ND4L_pos1, ND5_pos1, ND4_pos1
2 | GTR+I+G | 1263 | 155318824bc296f187855e732e0e635d | 16S
3 | GTR+I+G | 945 | 4e1808ec264e2fa3f30583199e2248af | ND2_pos1, ATP6_pos1, ATP8_pos2, ATP8_pos1, ND3_pos1, ND6_pos1
4 | TVM+I+G | 1604 | fff1365b3686e42fde9cee4aa61a98a1 | COI_pos2, COII_pos2, COIII_pos2, ATP6_pos2, CYTB_pos2
5 | TRN+I+G | 1944 | b83ac5fdc4787fa832392d2f73881e94 | CYTB_pos3, COI_pos3, COIII_pos3, ATP6_pos3, ND2_pos3, COII_pos3
6 | HKY+G | 327 | aa62a92a90a9f416aeed822c5200004d | ND6_pos3, ATP8_pos3, ND3_pos3
7 | GTR+I+G | 1382 | 4beb4cd4d44c2086ca63d3abc29c8879 | COI_pos1, CYTB_pos1, COII_pos1, COIII_pos1
8 | GTR+I+G | 1429 | ba11cdb28632d47b51f246bf15e4415b | ND1_pos2, ND4L_pos2, ND4_pos2, ND5_pos2
9 | TRN+I+G | 1429 | 8b8b114698f586191df2ca01c1762c48 | ND5_pos3, ND1_pos3, ND4_pos3, ND4L_pos3
10 | TVM+I+G | 611 | 2ab6a5acd991badff9c8786cdfec8ee2 | ND3_pos2, ND2_pos2, ND6_pos2
For Mrbayes partition
begin mrbayes;
charset Subset1 = 1-771 7015-7965\3 10672-10959\3 10960-12678\3 9343-10671\3;
charset Subset2 = 772-2034;
charset Subset3 = 7966-8985\3 2035-2700\3 2702-2868\3 2701-2868\3 8986-9342\3 12679-13134\3;
charset Subset4 = 2870-4407\3 4409-5085\3 5087-5871\3 2036-2700\3 5873-7014\3;
charset Subset5 = 5874-7014\3 2871-4407\3 5088-5871\3 2037-2700\3 7968-8985\3 4410-5085\3;
charset Subset6 = 12681-13134\3 2703-2868\3 8988-9342\3;
charset Subset7 = 2869-4407\3 5872-7014\3 4408-5085\3 5086-5871\3;
charset Subset8 = 7016-7965\3 10673-10959\3 9344-10671\3 10961-12678\3;
charset Subset9 = 10962-12678\3 7017-7965\3 9345-10671\3 10674-10959\3;
charset Subset10 = 8987-9342\3 7967-8985\3 12680-13134\3;
partition PartitionFinder = 10:Subset1, Subset2, Subset3, Subset4, Subset5, Subset6, Subset7, Subset8, Subset9, Subset10;
set partition=PartitionFinder;
lset applyto=(1) nst=6 rates=invgamma;
lset applyto=(2) nst=6 rates=invgamma;
lset applyto=(3) nst=6 rates=invgamma;
lset applyto=(4) nst=6 rates=invgamma;
lset applyto=(5) nst=6 rates=invgamma;
lset applyto=(6) nst=2 rates=gamma;
lset applyto=(7) nst=6 rates=invgamma;
lset applyto=(8) nst=6 rates=invgamma;
lset applyto=(9) nst=6 rates=invgamma;
lset applyto=(10) nst=6 rates=invgamma;
Why the set 9 and 10 have the substitution model nst=6 (GTR model) as the other subsets? while the set 6 change correctly to nst= 2 (HKY Model)
thank for your advises
KS