Confusion on -theta flag ?

[brycejoh16]

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]

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.