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Bayesian Evolutionary Analysis Sampling Trees
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Implementing more protein models into BEAUTI/BEAST #1184

Open JirkaMP opened 1 month ago

JirkaMP commented 1 month ago

Hi everyone, I'm very new to the BEAST community and tumbled across an issue. Using IQtree's ModelFinder, I identified the best protein substitution models for a set of proteins I included in a phylogenetic analysis. Now, I would like to run a molecular dating analysis with BEAST including those protein models, so I created a nexus file containing my multiprotein alignment, regions that refer to each protein and their respective best models (see below):

The alignment was too long to add

begin sets; charset 38k = 1-699; charset ac81 = 700-1009; charset dnapol = 1010-3374; charset helicase = 3375-6193; charset lef4 = 6194-7531; charset lef8 = 7532-9533; charset lef9 = 9534-10914; charset p33 = 10915-11677; charset p47 = 11678-12851; charset p74 = 12852-13939; charset pif1 = 13940-14875; charset pif2 = 14876-15459; charset pif3 = 15460-15813; charset pif4 = 15814-16667; charset pif6 = 16668-17071; charset vp39 = 17072-17615; charset vp91 = 17616-19070; end;

begin assumptions; charset_model 38k = Q.pfam+F+I{0.0147265}+G4{1.30949}; charset_model ac81 = LG+F+I{0.0308603}+G4{1.61915}; charset_model dnapol = Q.pfam+F+I{0.0125308}+G4{1.47578}; charset_model helicase = Q.pfam+F+I{0.0034635}+G4{2.03655}; charset_model lef4 = Q.pfam+F+I{0.0219115}+G4{1.69875}; charset_model lef8 = Q.pfam+F+I{0.00791903}+G4{1.34902}; charset_model lef9 = VT+F+I{0.00778775}+G4{1.9748}; charset_model p33 = VT+F+I{0.00970993}+G4{2.68922}; charset_model p47 = Q.pfam+F+I{0.00839166}+G4{1.56855}; charset_model p74 = Q.pfam+F+I{0.0200284}+G4{1.70337}; charset_model pif1 = WAG+F+I{0.0197432}+G4{2.26165}; charset_model pif2 = WAG+F+I{0.0276439}+G4{1.4145}; charset_model pif3 = Q.yeast+I{0.0323176}+G4{1.1696}; charset_model pif4 = Q.pfam+F+I{0.0101419}+G4{1.25143}; charset_model pif6 = Q.yeast+G4{2.02776}; charset_model vp39 = LG+F+I{0.0149826}+G4{2.2551}; charset_model vp91 = WAG+F+I{0.0100864}+G4{2.99185}; end;

Importing the file into BEAUTI works with no issue, but I noticed that only the WAG model is available for the models that I would need, but all the others aren't available. My question, is there a way to implement these missing models (like VT or LG) or maybe a command line based approach to circumvent this restriction of BEAUTI?

Thank you for taking the time to read my post! Please let me know if I described my issue too superficially and if you require more information.

Best Jirka

GuyBaele commented 1 month ago

Hi Jirka,

While I don't think that all of these models are currently implemented in BEAST, some of them certainly are: BLOSUM_62, DAYHOFF, JTT, MT_REV_24, CP_REV_45, WAG, LG, FLU, MTVER, MTPRO, MTMET, MTINV, MTDEU and MTMAM.

I'm not sure why (some of) these models are not showing up in BEAUti but can certainly look into it. Could you e-mail me your input file in the meantime?

Best regards, Guy

JirkaMP commented 1 month ago

Dear Guy, Thank you for your rapid response! Please find attached the nexus file I use as input and a screenshot from my Beauti showing the available models I can choose from.

Cheers Jirka

Von: Guy Baele @.> Gesendet: Dienstag, 28. Mai 2024 15:08 An: beast-dev/beast-mcmc @.> Cc: Petersen, Jirka Manuel @.>; Author @.> Betreff: Re: [beast-dev/beast-mcmc] Implementing more protein models into BEAUTI/BEAST (Issue #1184)

Hi Jirka,

While I don't think that all of these models are currently implemented in BEAST, some of them certainly are: BLOSUM_62, DAYHOFF, JTT, MT_REV_24, CP_REV_45, WAG, LG, FLU, MTVER, MTPRO, MTMET, MTINV, MTDEU and MTMAM.

I'm not sure why (some of) these models are not showing up in BEAUti but can certainly look into it. Could you e-mail me your input file in the meantime?

Best regards, Guy

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GuyBaele commented 1 month ago

Hi Jirka,

I see all of those models that I mentioned when I run BEAUti, so I currently can't replicate what you're experiencing. Let's for the time being move this issue off of GitHub. Please contact me via e-mail - not by responding to this GitHub notification - so that we can look into this.

Best regards, Guy