Input alignment for Beast as an external *link* in the XML control file.
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3.9 years ago
BlastedBadger ▴ 160

I want to input an alignment (fasta format) for Beast2, but having to rewrite the entire data (8 million sites) into the XML file seems like a waste of space. Does anyone know if there is a syntax that would allow inputting the alignment from an external file?

As an example, I have the following files:

alignment.fasta              # 167M  (20 species, 8,718,120 nucleotide sites)
beast_dating_parameters.xml  # 170M

At the moment, I create the xml from a template using beastgen.

Beast Beast2 beastGen Beauti • 614 views
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