augur
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ENH: Allow use of nextalign in augur translate
Context
It'd be good if augur translate
could interface with nextalign.
We have an explicit_translation.py
script that does the job, but it'd be nice to integrate into translate
.
The script can be found here for example: https://github.com/neherlab/ncov-simple/blob/master/scripts/explicit_translation.py
Right now augur translate
asks for ancestrally reconstructed node data for internal nodes. The explicit translation script starts with the translations and infers internal nodes.