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
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