Confusion on -theta flag ?

debbiemarkslab / plmc

Inference of couplings in proteins and RNAs from sequence variation

MIT License

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Confusion on -theta flag ? #21

Open brycejoh16 opened 9 months ago

brycejoh16 commented 9 months ago

This may seem obvious, but does the -t flag of say 0.2 do the evolutionary reweighting for us?

I just feel like I'm always confused for all these methods ... EVE, EVMutation etc. if that is done for us, or we need to do that ourselves...

Sorry for the obvious question :/ Bryce

aaronkollasch commented 6 months ago

Hi Bryce, Sorry for the late reply,

That is correct, plmc reweights the sequences by default, using the theta parameter. EVE and EVcouplings do this as well, though it can be overridden for example in the EVE mappings file or EVcouplings config file.