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LinguList avatar LinguList commented on July 21, 2024

there's a better way for nexus output, but there's a bug for mrbayes, so you'll need to look into that or manually refine (or just ignore mrbayes commands):

In general, I recommend changing language names in the data.

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PhyloStar avatar PhyloStar commented on July 21, 2024

Okay. I prefer glottolog codes or ASJP style names. Or the length of the name field to be fixed like 40 characters something like PHYLIP is also fine.

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LinguList avatar LinguList commented on July 21, 2024

In fact, I checked, and when using lingpy.convert.strings.pap2nex instead of the simple output, we can add the taxa:

>>> wl = Wordlist('example.tsv')
>>> from lingpy.convert.strings import pap2nex
>>> taxa = [myglottoconverter[t] for t in wl.taxa]
>>> paps = wl.get_paps(ref='cogid/infomapid/whatever', missing="?")
>>> pap2nex(taxa, paps, filename="outputfile")

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LinguList avatar LinguList commented on July 21, 2024

This is the same as wl.output(*) but you can specify the language names.

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PhyloStar avatar PhyloStar commented on July 21, 2024

Okay. This is great. Thank you.

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