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The obtained chromatograms were analyzed and manually edited in the Chromas 2.4 software (Technelysium Pty Ltd., South Brisbane, Australia).
Forward and reverse reads for all regions were assembled and aligned using Geneious Pro (Biomatters, New Zealand), with the alignments being subsequently manually edited in BioEdit 7.1.3 (Hall 1999); inversions were offset and the final alignment was 6905 bases long, with 39 bases excluded due to alignment uncertainty.
Each sequence was manually edited in conjunction with its chromatogram.
These family alignments were manually edited in order to ensure the correct alignment of the transmembrane regions, as well as of other OR protein motifs (such as an N-glycosylation site).
Alignments were manually edited in MacClade.
Sequences were aligned and manually edited in SeqMan (DNASTAR , Inc.
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Alignments were manually edited if necessary.
For Ka/Ks analysis, the alignment was manually edited to remain in-frame, and stop codons in primate sequences were replaced by gaps.
The two scaffolds were manually edited together, resulting in the full gene sequence.
To ensure comparable data analyses, and to remain conservative in subsequent tests for positive selection, we applied several criteria to remove highly divergent sequences: we manually edited the alignments in BioEdit, removing unalignable N- and C- termini up to the first set of completely conserved amino acid residues.
Sequences were manually edited and quality-checked in Geneious (version 7.0.4, Biomatters Limited).
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