Hi all,

I am new into Detecting Positive Selection and I find in the literature this paper "Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level" from Zhang in the 2005.

there is a concept that I could not understand : foreground and background lineages

the context : " Yang and Nielsen (2002) introduced a branch-site method for testing positive selection on individual codons along specific lineages. In this test, branches of the tree are divided a priori into foreground and background lineages, and a likelihood ratio test (LRT) is constructed by comparing a model that allows positive selection on the foreground lineages with a model that does not allow such positive selection"

I understand that the foreground linage is like the Positive control, "there must show positive selection" and background lineages is the Negative control "there must not show positive selection"

but im not sure about this

thaks for the help