Dear joao,
Quote:Hello
Is there a maximum number of partitions that you can attribute to a dataset? I'm stuck with 5... Is there a way around that?
There is no limit of the number of partitions attached to any given dataset. If you are working through the graphical interface, there is a limit that any given site can only belong to 4 partitions (i.e. partitions may overlap, but not more than 4 deep).
Are you having trouble defining more than 5 partitions? If so I'd be interested to know how...
Quote:I'm not really familliar with those kind of analysis, and I'm extremely confused by the possible differences between some of the models tested in PAML, and the ones in hyphy. Is there major differences between the 2 programs for similar models?
Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
- major differences are discussed in the manuscript there (pgs 16-17). If you have questions about a specific model, I'll be happy to elaborate.
Quote:I guess that the "branch-site" model ("B") from PAML is implemented in hyphy, but where? Or do we have to define it?
Thanks for your time.
HyPhy does not include predefined analyses to implement the branch-site models by Yang and Nielsen. It defines model a-la Yang 1998 (i.e. branch specific selection) - details in Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
and some others. It wouldn't be too difficult to write a 'branch-site' model in the HyPhy batch language though - I can help you get started if you want.
HTH,
Sergei