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For phylogenetic analysis of the Cox proteins, TBLASTX searches were carried out, the corresponding sequences recovered from GenBank and a multiple alignment generated using Clustal X and manually refined as mentioned above.
These unusual genes structures were manually refined as appropriate.
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The final alignment has been manually refined at the variable N-terminus and used in the subsequent analysis.
It's pleasingly refined as well.
A multiple sequence alignment of the LI818-like sequences was generated as described above, and manually refined using BioEdit, on the basis of the crystal structure of the CAB from spinach (PDB code 1RWT; [ 42]).
The output was manually refined by visual inspection of the spectrograms so as to reach a classification of different call types according to the descriptions in Zann (1996).
Each trans-axial region-of-interest (ROI) was visually reviewed and manually refined if necessary.
Alignments were manually refined using phylogenetically conserved secondary structures.
Then the MSA was manually refined, taking into account the structural superimposition of the templates.
Nucleotide sequences were aligned with Clustal W version 1.4 [39] and manually refined using MacClade v4.05 software.
Amino acid sequences were aligned with ClustalX (version 1.83) [42] and manually refined with GeneDoc (version 2.6) [43].
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