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Gathering requirements should be fun. It's the brainstorming process refined. It shouldn't get in the way of productivity or creativity. Harvest is about gathering requirements in the most intuitive, least intrusive way possible.
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trimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment.
