Comments (5)
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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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.
from autocogphylo.
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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This is the same as wl.output(*)
but you can specify the language names.
from autocogphylo.
Okay. This is great. Thank you.
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Related Issues (14)
- LexStat HOT 11
- adjust pmi score creation to regular wordlist output HOT 12
- Number of clusters and number of characters in nexus files HOT 2
- Language names to glottocodes omitted languages. HOT 2
- Generalized quartet distance HOT 3
- Turchin HOT 11
- Pama-Nyungan HOT 11
- Mutual coverage reports HOT 2
- Sino-Tibetan data contains many errors and needs to be replaced HOT 1
- selection of subsets based on coverage HOT 32
- reference trees HOT 9
- improper segmentation in aa data HOT 1
- ASJP and DOLGO columns HOT 5
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