PMSF model selection

[RX ZHANG]

Hi there,

I'm using PMSF model for dealing with LBA problem. I have a question about selecting models.

I can understand the workflow in the paper and manual that 

1. build a guide tree with `LG+F+Γ` with is fast

2. build a PMSF tree based on it with `LG+C20+F+Γ` and use `-ft` to specify the guide tree file. 

My question is 

When I built a guide tree with `-m TEST` to try to make it accurate as mentioned in the paper. The optimum model I got is "VT+F+I+G4". Then, to use PMSF, what should I use here? Should I use "VT+F+I+G4+C20" or still use "LG+C20+F+Γ"?

Thank you in advance,

Ruixuan

[Minh Bui]

Hi Ruixuan,

Yes, you should better use VT+F+I+G4+C20 for your data. I’m just not sure if +I works with +C20. In case not, remove +I, i.e.: VT+F+G4+C20.

Cheers

Minh

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[RX ZHANG]

Hi Minh,

Thank you very much!!

Best regards,

Ruixuan