How can I interpret the result of ppred program inplemented in the software package of phylobayes?

26 December 2015 1 5K Report

Hello everyone! Recently, I was running phylobayes, I wondered that whether it makes sense to run ppred on the protein alignment with length of 118 AAs. I suppose that the length of the alignment is quite short and it may make no sense statistically. Does anyone can give suggestions? Thanks very much for any reply!

Steven Dodsworth

I think it's slightly difficult to interpret the result. I don't see why a short alignment of 118 AAs would be a problem, though - you will just reach saturation in the information bootstrapping can provide with fewer bootstraps. Do you suspect the model is inappropriate? I would rather test some different models and compare results, but it depends what you are doing I suppose.

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