I am trying to incorporate a small published UCE phylogeny into a larger UCE phylogeny that I am building. The small phylogeny is for a single genra in the family, and I am building a phylogeny for the entire family. The data is accessible here; https://datadryad.org/stash/dataset/doi:10.5061/dryad.j5n06
However, I am currently in the assembly stage and unsure how to incorporate the published UCEs into my pipeline. The published data does not include any fasta files, but has a nexus files containing each individual UCE loci from a complex matrix. Since all those loci are shared, can I generate a fasta file from the nexus file? Does anyone have any suggestions on how to proceed, or should I email the authors and ask for their contig files?
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