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Note ==== In TREE_PUZZLE (Schmidt et al. 2003) and PHYML (Guindon and Gascuel 2003) a dot/period (".") in a sequence is interpreted as meaning the same character as in the first sequence. The PHYLIP 3.6 documentation says: "a period was also previously allowed but it is no longer allowed, because it sometimes is used in different senses in other programs" At the time of writing, we do nothing special with a dot/period.
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PhylipWriter Phylip alignment writer. |
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PhylipIterator Reads a Phylip alignment file returning an Alignment object iterator. |
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