only a curious dub to Model in Partition finder

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Karen Salazar

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May 15, 2020, 7:09:19 PM5/15/20
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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

Rob Lanfear

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May 15, 2020, 7:12:24 PM5/15/20
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Hi Karen,

Good question, and a simple answer. The TRN and TVM models are not available in MrBayes, so GTR is a good replacement.

If you like you can re-run PartitionFinder with models=mrbayes, in which case PartitionFinder will only consider models that are available in MrBayes. It’s probably not necessary though, I very much doubt it will make any difference to your final analysis.

Rob


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Rob Lanfear
Division of Ecology and Evolution,
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The Australian National University,
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Karen Salazar

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May 18, 2020, 2:15:52 PM5/18/20
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Dear Rob, 
thank so much for the reply. I m new in this and I was in dub to continue the analysis without put these models.

Karen S

MNHN, Paris

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