What is the meaning of common and consensus? about panacus HOT 4 CLOSED

Hi Lan,

admittedly, these labels have been chosen somewhat arbitrarily. "Common" means that the corresponding node/base pair/edge appears in all accessions, whereas consensus counts those appearing in >=50%.

We are working on an entirely revised version that will be released soon where these labels can be set by the user.

-dany

from panacus.

Hi dany,

Thanks for your soon reply.

I have one more question.
Here, in the plot, least-squares fit to m*X^ (m=20331763.197, γ=0.811).
What can we get from this number?
Such as what the meaning of the higher m or higher γ?

Many thanks!
Lan

from panacus.

Typically, only the γ factor is of interest, it indicates wheather the pangenome is open or closed. γ takes on values between 0 and 1, those closer to 0 indicate a close pangenome, whereas those closer to 1 indicate an open pangenome. More details can be found here: https://doi.org/10.1016/j.mib.2008.09.006

from panacus.

Got it.
Thanks!

from panacus.