Hey everyone.

Sorry if this is a naive question, I'm new to this software package.  I just finished using Spidermonkey (through the webserver) to identify epistatic interactions between 73 sites in an alignment of 75 amino acid sequences (alignment length of 791).  I was very pleased with the results and I'd like to do some additional analyses with additional sites (maybe up to 120 or so at a time).

Because of the current limit on the webserver, I downloaded the most recent version of the HyPhy package.  My question is how can I run a spidermonkey analysis locally through the suite?  I already have a model selected (through cAIC) and a ML phylogeny generated (incorporated into my nexus formatted dataset).

Any guidance would be greatly appreciated.  Thanks!

Some quick searching led to this post on these very forums from 2009:

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I tried following the procedure referenced in this post, but I encountered an error because my dataset is comprised of sequences of amino-acids and not codons/nucleotides.  The webserver possesses the capacity to process my dataset, does the local version currently lack this capability?