missing PRIME online documentation

[kaw97]

Very minor issue, but I noticed the page for the PRIME documentation is dead. Is this a bug or is there no extra documentation? https://hyphy.org/methods/other/evo/PRIME.md

Additionally, PRIME requires a JSON file with amino acid properties. Does this need to be user-created/how does the JSON need to be formatted, or is one available?

[spond]

Dear @kaw97,

It does seem that the old documentation is dead; I need to update it. PRIME is one of these methods that has been "in development" for a decade, but never quite reaches the finish line. @hannahkimincompbio is actively working on it at this time, so perhaps she can help with more specific questions.

The properties file is require only if you want to use somethign other than the built-ins (Atchley, LCAP, Random), which is specified via the --properties option. If you give --properties Custom then you also need to supply --property-file. That's basically a JSON dictionary of the form

{
   "prop1 name" : {
         "A" : value,
         "C": value,
....
   }
...
}

like in https://github.com/veg/hyphy/blob/6674e219ffa22aa08330cce94e2731c99337bbe9/res/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf#L30

Best, Sergei

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