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#1838 updated the as_nexus method to make it more standards compliant. Before we release this in 0.4.0 we should (at least) decide whether we should include the alignments in the DATA block of the nexus file. (Like this example)
Since the as_nexus/write_nexus methods are new in 0.4.0 I guess we should either (a) output alignments in the DATA block or (b) document that we want to do this later and that the default will always be to not output the alignments. However, once we have #1825 merged it should be pretty straightforward to implement. I presume things like matchchar are optional?
@jeetsukumaran any thoughts here? Would it be expected that a nexus conversion should output the full data set by default, or just include the trees?
The text was updated successfully, but these errors were encountered:
I think would expect the entire dataset to be written out unless I specified otherwise (e.g., is_include_chars=False or is_exclude_chars=True, depending on which idiom you like, along with a parallel is_include_trees/is_exclude_trees).
#1838 updated the
as_nexus
method to make it more standards compliant. Before we release this in 0.4.0 we should (at least) decide whether we should include the alignments in the DATA block of the nexus file. (Like this example)Since the as_nexus/write_nexus methods are new in 0.4.0 I guess we should either (a) output alignments in the DATA block or (b) document that we want to do this later and that the default will always be to not output the alignments. However, once we have #1825 merged it should be pretty straightforward to implement. I presume things like
matchchar
are optional?@jeetsukumaran any thoughts here? Would it be expected that a nexus conversion should output the full data set by default, or just include the trees?
The text was updated successfully, but these errors were encountered: