Re: PartitionFinder (Beauti)

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Rob Lanfear

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Jun 26, 2020, 1:05:39 AM6/26/20
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Hi Elvis,

This is a question for the BEAST usergroup I think. Though my suggestion would be to just keep the mt and the nuclear genes separate, since as far as I'm aware BEAST doesn't allow for the mixtures of ploidy that would be required to model the best partitioning scheme found by PartitionFinder.

Rob

On Wed, 10 Jun 2020 at 08:27, Elvis Almeida <elvis...@gmail.com> wrote:
Hey, I need help!

I checked the substition models for my genes in PartitionFinder, inserting these partitions in Beauti 1.8.0 to run a speciestree in *Beast, however, in the "trees" tab (attached figure) of Beauti I don't know what to put in the "Ploidy type" tab (autosomal nuclear, X, Y or mitochondrial). Whereas, some partitions (below) generated by PartitionFinder grouped mitocontrial and nuclear genes. What do I need to do in this case?


Subset | Best Model | # sites    | subset id                        | Partition names                                                                                     
1      | TRN+I+G+X  | 2179       | f13084f85bc0406c8f73205d5acf0a80 | 16S, RAG2, POMC, 12S                                                                                
2      | TRN+G+X    | 657        | d69cf481cf11834d424373588f964708 | COI, RAG2                                                                                           
3      | TRN+I+G+X  | 405        | 8b49312cf222adddfd113a219e4f437a | ND1, Cytb                                                                                           
4      | TRNEF+I    | 1258       | 8f28186f6e2733c99c93a7bcbcb83fa5 | CXCR4, ND1, CXCR4, TNS3, ND2, Cytb, POMC                                                            
5      | HKY+X      | 496        | f68ceff8830035c70fc87bbba2e34d08 | Cytb, CXCR4, ND2                                                                                    
6      | TRN+I+X    | 287        | aba8e28b6bf6cf9cbd3499480f3d803a | ND1                                                                                                 
7      | HKY+X      | 173        | 7e157502e3de1aea743aeaa56b4a14ff | ND2                                                                                                 
8      | HKY+X      | 437        | 23f55160c0ca2b4e2b481d61f8cc829f | TNS3, TNS3, POMC                                                                                    
9      | TRNEF+G    | 662        | 6e8696bd967c9720f1fc7b016ada7171 | TYR, RAG2, TYR, TYR                                                                                 
10     | JC         | 263        | 8c1a6b7c5965d448465ff9234d70eec5 | RAG1, RAG1, RAG1  

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Rob Lanfear
Division of Ecology and Evolution,
Research School of Biology,
The Australian National University,
Canberra
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