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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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concatenate with character sets in Phyluce 1.7.1 #319

Closed JennaMcCullough closed 8 months ago

JennaMcCullough commented 8 months ago

I'm running v. 1.7.1 and trying to get a concatenated phylip alignment with character sets. The script to concatenate alignments in the newer version, Phyluce_align_concatenate_alignments, does not have a character sets flag. I used to be able to use phyluce_align_format_nexus_files_for_raxml which did have a flag to produce a character sets flag (--charsets). Is there a reason why it was removed in the newer version, or am I just not seeing the script that would produce this output in addition to a concatenated alignment?

Thanks in advance

Jenna

JennaMcCullough commented 8 months ago

Well, I realize now that the character sets are just default. Whoops.

brantfaircloth commented 8 months ago

🤣 no worries

JennaMcCullough commented 8 months ago

🤦‍♀️