# File listing

* hymenoptera-uce-probes.fasta
* in-silico-NOTES.txt
* in-silico-contigs.tar.gz
* in-silico-uce-probes-to-contigs.lastz.tar.gz
* in-silico-taxon-set-alignment-data.tar.gz
* hymenoptera-data-sets.conf

* abyss-NOTES.txt
* abyss-contigs.tar.gz - UCE contigs enriched from hymenopteran taxa and assembled using ABySS.
* abyss-uce-probes-to-contigs.lastz.tar.gz - LASTZ files showing mapping of UCE probes onto in silico genome slices AND probe.matches.sqlite database.
* abyss-assembly-and-probe-alignment-logs.tar.gz - Log files from ABySS probe alignment.
* abyss-taxon-set-alignment-data.tar.gz - Archive file containing nested directories of ABySS alignment and analysis data.  See overall README or file-specific README.

* trinity-NOTES.txt - NOTES describing the pipeline steps used to analyze the TRINITY data.
* trinity-contigs.tar.gz - UCE contigs enriched from hymenopteran taxa and assembled using TRINITY.
* trinity-uce-probes-to-contigs.lastz.tar.gz - LASTZ files showing mapping of UCE probes onto TRINITY contigs AND probe.matches.sqlite database.
* trinity-assembly-and-probe-alignment-logs.tar.gz - Log files from TRINITY probe alignment.
* trinity-taxon-set-alignment-data.tar.gz - Archive file containing nested directories of TRINITY alignment and analysis data.  See overall README or file-specific README.

* in-silico-RENAMED-TIPS.tree - In silico tree with tips renamed to full species binomial
* abyss-WITH-SAWFLIES-100-bootrep-RENAMED-TIPS.tree - ABySS (with sawfly taxa) tree with tips renamed to full species binomial
* trinity-WITH-SAWFLIES-100-bootrep-RENAMED-TIPS.tree - Trinity (with sawfly taxa) tree with tips renamed to full species binomial
* trinity-WITHOUT-SAWFLIES-100-bootrep-RENAMED-TIPS.tree - Trinity (*without* sawfly taxa) tree with tips renamed to full species binomial

* Tables.xlsx - Excel file of tables in manuscript.
* figure-1-hymenoptera-with-sawflies.ai - Illustrator file of Figure 1.
* figure-1-photoshop-images.tar.gz - Archive of photoshop cartoon images used in Figure 1.
* figure-1-image-sources.txt - Sources of Figure 1 images.
* supplemental-figures.tar.gz - Archive of supplemental figures (Illustrator documents).
* pycogent-distance-estimates.xlsx - Distances estimates output by PyCogent as xlsx file.
* r-steps-and-data.tar.gz - Steps and data used in R for barplots and glms.
 
* README

# Data archived elsewhere

* Raw sequence reads reads are available from SRA:
    * SRA SRP042397
    * BioProject PRJNA248919

* Trinity contigs from taxa are awaiting GenBank accessions (also available from this repository)

# Software

We conducted analyses using _phyluce_ 1.4 or greater (exact commit denoted by hash in log files).  _phyluce_is available from:

* http://github.com/faircloth-lab/phyluce

We also used:

* http://github.com/faircloth-lab/illumiprocessor
* https://github.com/faircloth-lab/uce-probe-design


# Data archives with nested structure

There are several archives that contain nested directories.  Below, we have those archives and what those archives contain.  The gzipped tar files that contain directories or other nested files are:

* in-silico-taxon-set-alignment-data.tar.gz
* abyss-taxon-set-alignment-data.tar.gz
* trinity-taxon-set-alignment-data.tar.gz

## 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.


## 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.


## 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.