Hi
I have recently found out about HyPhy and am still trying to understand its capabilities. It is possible to recontruct ancestral sequences with HyPhy?


Thanks

Slim Sassi

Dear Slim,

Yes it is possible to reconstruct ancestral sequences with HyPhy (using almost any model of substituion you can define in HyPhy).

Typically one would fit a model using some standard analyses (e.g. Basic analyses->AnalyzeNucProtData.bf), then use Analyses->Results->Ancestral Sequences to reconstruct ancestors and save them to a file. The above works for GUI versions on Mac and Windows.

For command line HyPhy, use the '-p' flag on the command line to invoke result processors after an analysis is complete.

If you wish to reconstruct ancestors in custom written analyses, you may want to take a look at this command:Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login


HTH,
Sergei

Dear Sergei,

Thanks for the reply.
Does HyPhy implement only joint reconstructions? How about marginal reconstrcutions?

Thanks

SLim

Does HyPhy implement only joint reconstructions? How about marginal reconstrcutions?

HyPhy only implements 'joint' reconstructions: this seems to be the sensible approach to take. See Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for discussion.

It appears to me that the reason marginal reconstruction was used in the past could be that in the 1990's there was did not exist an efficient (fast) algorithm for the joint ancestral reconstrucion.

Cheers,
Sergei