Hi!
I was trying to make the phylogenetic inference and selection pressure analysis with HYPHY package, because the DataMonkey don't accepted dataset whit 250 sequences   :)
I made following these steps:  Analysis -> Standard Analysis -> Phylogeny Reconstruction -> NJ.bf -> Full Likelihood -> Nucleotide/Protein -> My dataset -> I chose: first GRM model, second HKY -> I chose: first Global with variation +HM, second Global with variation, third Global, fourth Local -> Gamma (when necessary ) 4-> I chose: force to 0 and second keep negative and the following errors appear:
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Anyone can help-me? ;D

Dear Jackson,

HyPhy is not reading your datafile properly, it seems (0 estimates tells me that it read '0' sequences).

First, try to open this data file using File->Open Data File. If all goes well, you should see a graphical data panel with your sequences. Look at the documentation for the list of formats HyPhy can read.

Also, I recommend you use Distances in place of Full Likelihood when building neighbor joining trees - the speed difference will be at least 100x.

Cheers,
Sergei