## in-silico-taxon-set-alignment-data.tar.gz ### Directory structure taxon-sets/ INSILICO-INCOMPLETE/ exploded-by-taxon/ INSILICO-INCOMPLETE.conf INSILICO-INCOMPLETE.incomplete mafft-nexus-min-10-taxa/ mafft-nexus-notrim-clean/ mafft-nexus-trimal-nexus/ informative-sites.csv INSILICO-INCOMPLETE.fasta log/ mafft-nexus-notrim/ mafft-nexus-trimal/ mafft-raxml/ ### File/Directory description * INSILICO-INCOMPLETE.conf: The loci output by get_match_counts.py for the taxa in in-silico-hymenoptera-taxon-sets.conf. * INSILICO-INCOMPLETE.fasta: Monolithic fasta file of UCE loci for the taxa in INSILICO-INCOMPLETE.conf. * INSILICO-INCOMPLETE.incomplete: A list of the missing loci among the taxa in INSILICO-INCOMPLETE.conf. * exploded-by-taxon/ - Directory containing species-specific FASTA files (the contents of INSILICO-INCOMPLETE.fasta exploded by taxon). * mafft-nexus-notrim/ - Untrimmed MAFFT alignments of the data in INSILICO-INCOMPLETE.fasta. * mafft-nexus-notrim-clean/ - Untrimmed MAFFT alignments of the data in INSILICO-INCOMPLETE.fasta stripped of the UCE locus name. * mafft-nexus-trimal/ - Trimmed versions of the MAFFT aligments in mafft-nexus-notrim-clean/. * mafft-nexus-trimal-nexus/ - Trimmed versions of the MAFFT aligments in mafft-nexus-notrim-clean/ converted to NEXUS format. * mafft-nexus-min-10-taxa/ - Trimmed versions of the MAFFT aligments in mafft-nexus-notrim-clean/ converted to NEXUS format limited to those containig 10 taxa or more. * informative-sites.csv - The number of informative sites across alignments in mafft-nexus-min-10-taxa/. * log/ - Log files output by PHYLUCE for various analyses. * mafft-raxml/ - Concatanated PHYLIP file for loci in mafft-nexus-min-10-taxa/ and RAxML results.