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Tests of positive selection were made by comparing the branch-site model A in which ω (dn/ds) ≥ 1 (alternative hypothesis) to the model A in which ω = 1 fixed (null hypothesis) and setting the foreground branch to the base of the clade containing the relaxin family orthologue in teleosts and the background branch was set to the same orthologue in mammals or vice versa [ 54].
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Each of the seven terminal branches was set up as foreground separately, whereas all other branches were designated as background at that time.
Negative branches were set to be zero.
The background correction was set to: offset = 50.
The background density was set to 0 g/cm3.
The background threshold was set at twice the background fluorescent signal plus 3 standard deviations.
Each branch length was set as the number of events occurring along the branch.
Background white noise was set at 70 dB.
A branch of Syriatel in Deraa was set on fire.
In this model, the foreground branches are the branches tested for positive selection, and the background branches are all other branches on the tree [ 48].
A branch-site codon model allows the ω rate ratio to vary along the sequence in some pre-specified branches, called the foreground branches, while the ratio in the other branches, or background branches, is kept constant and < 1 [ 47].
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CEO of Professional Science Editing for Scientists @ prosciediting.com