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FePhyFoFum / phyx

phylogenetics tools for linux (and other mostly posix compliant) computers
blackrim.org
GNU General Public License v3.0
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Nexus writer: INTERLEAVE=NO is not valid #155

Closed josephwb closed 3 years ago

josephwb commented 3 years ago

The keyword INTERLEAVE is a switch to turn on. INTERLEAVE=NO is thus not supported, and any program that uses the NCL (e.g., iqtree) will error. MrBayes, however, allows interleave=yes and interleave=no, and this doc suggests that it is valid usage. FWIW PAUP* opens such files fine.

I guess we should remove any =yes/no from this keyword.

josephwb commented 3 years ago

Trying to get feedback from the original/NCL authors on what is best to do. I think ideally NCL would support both forms, but they might be hesitant to do something that was not expressed in the original paper (which is a simple switch).

josephwb commented 3 years ago

FWIW on ingest phyx supports both flavours. So it is only export that we need to worry about.

josephwb commented 3 years ago

Hrm, to be on safe side just removed INTERLEAVED=NO from write_nexus_alignment with eea8dfc.