Dear walter,

DirectionalREL.bf expects a protein (not a codon) alignment. Could you verify that's what you were inputting?

Cheers,
Sergei

Dear Walter,

Could you attach (or e-mail to me) the alignment file that causes DirectionalREL.bf to throw an error message so that I can reproduce the error and try to debug it? The error report suggests that HyPhy is reading your alignment as something other that proteins (this is why the incompatible dimensions error), and I am not sure why.

Also, which analysis options did you select for DirectionalREL.bf?

Cheers,
Sergei

Dear Walter,

Hmm; looks like when you save a protein file from the HyPhy datapanel, HyPhy incorrectly generates the NEXUS header by claiming this to be a DNA datafile, e.g

Code:

FORMAT
		DATATYPE = DNA

		GAP=-
		MISSING=?
	;
 

when of course DATATYPE=PROTEIN should be used. Thanks for pointing out this erroneous HyPhy behavior; I have fixed it in our development code already (this will be included in the next s/w release). If you edit the NEXUS file and change DNA to PROTEIN, the problem will disappear.

Before the next version of code is released, I would suggest doing this to avoid the issue: in the datapanel, make a partition using the entire dataset, and then click on the 'Save Partition To Disk' button to export the file (see sections 2.3.2 and 2.3.3 in Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login)

Cheers,
Sergei