The null assumption H0 of the LRT corresponds to the assumption that sequences in the multiple alignment had evolved according to the simpler M0-model.
Further, since the gene tree did not fully resolve relations between the Rap1 genes [Additional file 3: Supplemental Figure S3], we assumed that orthologs in the alignment have evolved along the branches of the established species phylogeny [ 28] (see Methods).
We therefore assumed that orthologs in the alignment have evolved along the branches of the established species phylogeny and confirmed that the computation of ω values is not sensitive to different basal branching patterns.
The ZNF507 fingerprint alignments could suggest that the protein has evolved to favor different DNA-binding motifs in each species; alternatively (or perhaps additionally), they could point plainly to three conserved ZNF motifs as having the most essential regulatory roles.
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