The alignment
step in phylogenetic analysis is one of the most important because it produces the data set on which models
of evolution are used.
It is not
uncommon to edit the alignment, deleting
unambiguously aligned regions and inserting or deleting gaps to more accurately reflect
probable evolutionary
processes that led to the divergence between sequences.
It is useful to
perform phylogenetic analyses based on a series of slightly modified alignments to determine how ambiguous regions in the
alignment affect the
results and what aspects of the results one may have more or less confidence in.Notices
of multiple sequence alignment