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broadinstitute / viral-phylo

viral-ngs: phylogenetics, annotation, intrahost variants
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add optional mafft speed up for closely related genomes #11

Open dpark01 opened 4 years ago

dpark01 commented 4 years ago

For mafft multichr, accept an optional reference genome or reference MSA and utilize the new —addfragments option outlined here https://mafft.cbrc.jp/alignment/software/closelyrelatedviralgenomes.html (but make it optional: not all viral species would be appropriate for this)

tomkinsc commented 4 years ago

As written we'll need to add new kwargs to maffy.py::execute() for --addfragments and --keeplength