Does the length of my sequence influence the shape of my Taxon ID Tree?
Short sequences may influence the shape of the Taxon ID Tree based on the alignment algorithm selected while building the tree. The BOLD Aligner is amino acid based, so instead of comparing the nucleotides between the sequences, it compares the amino acid translations. Using this alignment algorithm, short sequences are less likely to align correctly with longer sequences.
When building Taxon ID Trees containing short sequences (anything shorter than 200bp), it is recommended to use Muscle or Kalign algorithms. Independent of the alignment algorithm selected, whenever short sequences are included in an analysis, the results should be interpreted with caution.
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