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More details on the estimated omega for each cluster with codons under positive selection, position of every codon under positive selection, and results of the LRT for those clusters can be found in Additional file 3.
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Nevertheless, interspersed within this highly conserved domain several AA sites were assigned to class 3 with high probabilities (P > 0.95) suggesting that they are under positive selection (Positions 639, 650, 760).
Due to the inaccurate detected target location and the fixed selection positions in[1], the positive sample is sub-optimal, but one of the negative samples is the actually the "tracked target".
Opinions were broad, with limited overlap, reflecting scientific uncertainties about: the optimal form or combination of placental transfusion techniques; case selection; positioning of the baby; duration of delay, and timing of uterotonics.
Then, according to the order of selection, post positions were chosen.
The phylogenetic analysis showed strong positive selection at position 35 as the epitope changed from I to M to V (AKNI, unpublished data).
The SLAC method revealed one positive selection site (position 549) and 94 negative selection sites (P < 0.05) (Fig. 5a).
A unique amino acid has been found under positive selection at position 427, in the guanylate binding protein, C-terminal domain (Additional file 12: Figure S4D).
Two amino acids were found under positive selection at positions 191 and 370.
Intriguingly, the identified sites under positive selection include positions 55, 62 and 122, which are polymorphic in Atlantic cod; amino acid substitutions at two of these positions in avian hemoglobin seem to offer a selective advantage in air-breathing vertebrates.
Purifying selection at position 8 and 26 is fully consistent with the fact that these positions are part of the WD-repeat consensus [31].
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