## trinity-taxon-set-alignment-data.tar.gz

### Directory structure

taxon-sets/
    trinity-kmer1-WITHOUT-SAWFLIES-incomplete/
        informative-sites.csv
        mafft-nexus-min-30-taxa
        mafft-nexus-notrim-clean
        mafft-nexus-trimal-nexus
        remove_locus_name_from_nexus_lines.log
        trinity-kmer1-WITHOUT-SAWFLIES-incomplete.fasta
        log
        mafft-nexus-notrim
        mafft-nexus-trimal
        mafft-raxml
        trinity-kmer1-WITHOUT-SAWFLIES-incomplete.conf
        trinity-kmer1-WITHOUT-SAWFLIES-incomplete.incomplete
taxon-sets/
    trinity-kmer1-WITH-SAWFLIES-incomplete/
        contig-coverage
        log
        mafft-nexus-notrim-clean
        mafft-pycogent
        trinity-kmer1-WITH-SAWFLIES-incomplete.fasta
        exploded-by-taxon
        mafft-nexus-min-33-taxa
        mafft-nexus-trimal
        mafft-raxml
        trinity-kmer1-WITH-SAWFLIES-incomplete.incomplete
        informative-sites.csv
        mafft-nexus-notrim
        mafft-nexus-trimal-nexus
        trinity-kmer1-WITH-SAWFLIES-incomplete.conf

### File/Directory description

#### trinity-kmer1-WITHOUT-SAWFLIES-incomplete/

* trinity-kmer1-WITHOUT-SAWFLIES-incomplete.conf: The loci output by get_match_counts.py for the taxa in hymenoptera-data-sets.conf.
* trinity-kmer1-WITHOUT-SAWFLIES-incomplete.fasta: Monolithic fasta file of UCE loci for the taxa in trinity-kmer1-WITHOUT-SAWFLIES-incomplete.conf.
* trinity-kmer1-WITHOUT-SAWFLIES-incomplete.incomplete: Monolithic fasta file of UCE loci for the taxa in trinity-kmer1-WITHOUT-SAWFLIES-incomplete.conf.
* mafft-nexus-notrim: Untrimmed MAFFT alignments of the data in trinity-kmer1-WITHOUT-SAWFLIES-incomplete.fasta.
* mafft-nexus-notrim-clean: Untrimmed MAFFT alignments of the data in trinity-kmer1-WITHOUT-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-30-taxa: Trimmed versions of the MAFFT aligments in mafft-nexus-notrim-clean/ converted to NEXUS format limited to those containig 30 taxa or more.
* informative-sites.csv: The number of informative sites across alignments in mafft-nexus-min-30-taxa/.
* remove_locus_name_from_nexus_lines.log: Errant log file I forgot to put in log/.
* log: Log files output by PHYLUCE for various analyses.
* mafft-raxml: Concatanated PHYLIP file for loci in mafft-nexus-min-30-taxa/ and RAxML results.

#### trinity-kmer1-WITH-SAWFLIES-incomplete/

* contig-coverage: Coverage computation across assembled contigs.
* trinity-kmer1-WITH-SAWFLIES-incomplete.conf: The loci output by get_match_counts.py for the taxa in hymenoptera-data-sets.conf.
* trinity-kmer1-WITH-SAWFLIES-incomplete.fasta: Monolithic fasta file of UCE loci for the taxa in trinity-kmer1-WITH-SAWFLIES-incomplete.conf.
* trinity-kmer1-WITH-SAWFLIES-incomplete.incomplete: Monolithic fasta file of UCE loci for the taxa in trinity-kmer1-WITH-SAWFLIES-incomplete.conf.
* exploded-by-taxon: Directory containing species-specific FASTA files (the contents of trinity-kmer1-WITH-SAWFLIES-incomplete.fasta exploded by taxon).
* mafft-nexus-notrim: Untrimmed MAFFT alignments of the data in trinity-kmer1-WITH-SAWFLIES-incomplete.fasta.
* mafft-nexus-notrim-clean: Untrimmed MAFFT alignments of the data in trinity-kmer1-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-30-taxa/ and RAxML results.
* mafft-pycogent: pycogent output files.