Re: How to remove third codon position in doing analyses

[Rob Lanfear]

Hi There,

For this you should edit your alignment to remove the third codon positions. As far as I know this is the only way that will work for MrBayes.

If you want to be rigorous about it (and particularly if some of your subsets include 3rd codon positions along with other codon positions) then you should also re-run PartitionFinder after removing the third codon positions from your alignment as well.

Rob

On Tuesday, 29 August 2023 at 17:55:05 UTC+10 vijaya...@gmail.com wrote:

Hi,

I have 13 Protein coding genes (PCGs) and 2 non-coding genes. I divided the PCGs into all three codon positions. The following is the result. However, I don't want to use the third codon position in MrBayes. How do I do it? Kindly help. Here I would like to delete subset 3 and subset 8 because these two subsets had the third codon positions of all thirteen PCGs 

begin mrbayes;

charset Subset1 = 1-1539\3;
charset Subset2 = 2-1539\3;
charset Subset3 = 10071-10419\3 10422-11502\3 1542-2241\3 3-1539\3 9294-10068\3 3213-4167\3;
charset Subset4 = 1540-2241\3 9292-10068\3 3211-4167\3 4687-5847\3;
charset Subset5 = 9293-10068\3 1541-2241\3 3212-4167\3 4688-5847\3;
charset Subset6 = 11503-13068 13069-14186 2242-2463\3;
charset Subset7 = 10420-11502\3 5848-6156\3 10069-10419\3 2464-3210\3 7543-9291\3 4168-4686\3 6157-7542\3 2243-2463\3;
charset Subset8 = 7545-9291\3 6159-7542\3 4170-4686\3 2244-2463\3 2466-3210\3 4689-5847\3 5850-6156\3;
charset Subset9 = 10070-10419\3 10421-11502\3 4169-4686\3 7544-9291\3 6158-7542\3 5849-6156\3 2465-3210\3;

partition PartitionFinder = 9:Subset1, Subset2, Subset3, Subset4, Subset5, Subset6, Subset7, Subset8, Subset9;
set partition=PartitionFinder;

lset applyto=(1) nst=6 rates=gamma;
lset applyto=(2) nst=2 rates=propinv;
lset applyto=(3) nst=2 rates=invgamma;
lset applyto=(4) nst=2 rates=invgamma;
lset applyto=(5) nst=6 rates=invgamma;
lset applyto=(6) nst=6 rates=invgamma;
lset applyto=(7) nst=2 rates=invgamma;
lset applyto=(8) nst=2 rates=invgamma;
lset applyto=(9) nst=6 rates=gamma;

prset applyto=(all) ratepr=variable;
unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all) tratio=(all);

end;

[张东]

Hi,

You can also check this protocol: https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.87, it can fully satisfy your requirements.

Best, 

Dong

VijayaSai A <vijaya...@gmail.com> 于2023年8月29日周二 15:55写道：

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