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The comparison programs for pairwise comparison,
such as gap
must be run with the "out"
option in order to generate files suitable for manual alignment:
% gap -out
See the section on pairwise comparison for details of presentation
of the output. As described
in the description of the
lineup editor above ,
sequence files are loaded into 'lineup' with
the get
command. The manipulation of the .out files is straightforward.
NOTE: The manual creation of multiple sequence alignments might be
considerably influenced
by the user and is not recommended for
publication or tree creation.
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