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AlignIO now interleaves (wraps) large Nexus alignments to avoid long …
…lines. This should allow it to be used with MrBayes, while continuing to output non-interleaved Nexus for smaller alignments where there have been no issues reported. See mailing list dicussions: http://lists.open-bio.org/pipermail/biopython-dev/2010-December/008487.html http://lists.open-bio.org/pipermail/biopython/2013-March/008457.html
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