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We collected all motifs of 6 to 12 base pair length from ungapped (upper case) alignment columns.
In the latter case alignment information (position and length of gaps) can be imported back into the annotated dataset in ProSeq3.
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In each case, alignments showed extended regions of 100% or near 100% amino acid identity beginning at the site indicated.
The selection of taxa varied depending on each particular case (alignments and trees are available from the author upon request).
In these cases, alignment stops when both axes become parallel (limbs become parallel on standing films).
While this may be possible in a subset of cases, alignment of non-coding barcoding regions will be generally intractable across broader levels of phylogeny.
3' Tail ΔG Alignment Score: This score measures the worst-case alignment of the 3' tail of one primer along any other part of another sequence.
In all cases, alignment was unambiguous with no indels or frameshift mutations.
All the test-cases, alignment output and python scripts used in this study are hosted at (http://cage.unl.edu/DataPeptide).edu/DataPeptide
In these cases, alignments will be poor and phylogenetic analyses may be prone to long-branch attraction.
For uncertain cases, alignments with T-Coffee [39] and different ClustalW parameters were compared to combine them into a final alignment.
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CEO of Professional Science Editing for Scientists @ prosciediting.com