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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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phyluce_align_concatenate_alignments not found #220

Closed GillianGibb closed 3 years ago

GillianGibb commented 3 years ago

Hi, when using the programme phyluce_align_concatenate_alignments I get the error 'command not found'. Everything else I've trialled in the UCE tutorial 1 seems to be working fine.

brantfaircloth commented 3 years ago

the correct program name for now is phyluce_align_format_nexus_files_for_raxml. there is an update soon on the horizon where the name changes to phyluce_align_concatenate_alignments. the name change just made it into the documentation a little bit early.

GillianGibb commented 3 years ago

Aha! thanks, knew it would be something like this.

brantfaircloth commented 3 years ago

This problem should be fixed - I just released the new version of phyluce (1.7.0) and the documentation should reflect use of that version.

rbolem commented 11 months ago

the phyluce_align_format_nexus_files_for_raxml not works for phylip in this code phyluce_align_concatenate_alignments \ --alignments mafft-gblocks-70p \ --output mafft-gblocks-70p-raxml \ --log-path log --phylip