## abyss-taxon-set-alignment-data.tar.gz ### Directory structure taxon-sets/ abyss-WITH-SAWFLIES-incomplete/ abyss-WITH-SAWFLIES-incomplete.conf abyss-WITH-SAWFLIES-incomplete.incomplete exploded-by-taxon log mafft-nexus-notrim mafft-nexus-trimal mafft-raxml abyss-WITH-SAWFLIES-incomplete.fasta contig-coverage informative-sites.csv mafft-nexus-min-33-taxa mafft-nexus-notrim-clean mafft-nexus-trimal-nexus ### File/Directory description * contig-coverage: UCE coverage computation across assembled contigs. * abyss-WITH-SAWFLIES-incomplete.conf: The loci output by get_match_counts.py for the taxa in hymenoptera-data-sets.conf. * abyss-WITH-SAWFLIES-incomplete.fasta: Monolithic fasta file of UCE loci for the taxa in abyss-WITH-SAWFLIES-incomplete.conf. * abyss-WITH-SAWFLIES-incomplete.incomplete: A list of the missing loci among the taxa in abyss-WITH-SAWFLIES-incomplete.conf. * exploded-by-taxon: Directory containing species-specific FASTA files (the contents of abyss-WITH-SAWFLIES-incomplete.fasta exploded by taxon). * mafft-nexus-notrim: Untrimmed MAFFT alignments of the data in abyss-WITH-SAWFLIES-incomplete.fasta. * mafft-nexus-notrim-clean: Untrimmed MAFFT alignments of the data in abyss-WITH-SAWFLIES-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-33-taxa: Trimmed versions of the MAFFT aligments in mafft-nexus-notrim-clean/ converted to NEXUS format limited to those containig 33 taxa or more. * informative-sites.csv: The number of informative sites across alignments in mafft-nexus-min-33-taxa/. * log: Log files output by PHYLUCE for various analyses. * mafft-raxml: Concatanated PHYLIP file for loci in mafft-nexus-min-33-taxa/ and RAxML results.