The data in this directory corresponds to:
Skinner, R.K., Dietrich, C.H., Walden, K.K.O., Gordon, E., Sweet, A.D., Podsiadlowski, L., Petersen, M., Simon, C., Takiya, D.M., and Johnson, K.P.
Phylogenomics of Auchenorrhyncha (Insecta: Hemiptera) using Transcriptomes: Examining Controversial Relationships via Degeneracy Coding and Interrogation of Gene Conflict.
Systematic Entomology.

Correspondance should be directed to: Rachel K. Skinner, rskinn2@illinois.edu

If you use these data, please cite our paper in Systematic Entomology.

The following files can be found in this dataset:

Amino_acid_concatenated_alignment.phy: the amino acid alignment used in this analysis in phylip format.
Amino_acid_raxml_partitions.txt (for reference only): the partitions for the amino acid alignment, but a partitioned amino acid analysis was not performed in this study.
Amino_acid_concatenated_tree.newick: the best maximum likelihood tree with bootstrap values in newick format.

ASTRAL_input_gene_trees.tre: the concatenated gene tree input file for ASTRAL
README_pie_charts.md: explains the the scripts and data needed to recreate the pie charts figure from our paper. There is also another
Corresponds to the following files:
ASTRAL_species_tree_EN_only.newick: the species tree with only effective number (EN) annotation
ASTRAL_species_tree_pp1_only.newick: the species tree with only the posterior probability 1 (main topology) annotation
ASTRAL_species_tree_q1_only.newick: the species tree with only the quartet scores for the main topology (q1)
ASTRAL_species_tree_q2_only.newick: the species tree with only the quartet scores for the first alternative topology (q2)
ASTRAL_species_tree_q3_only.newick: the species tree with only the quartet scores for the second alternative topology (q3)
print_node_key_files.py: script needed to create the following files:
node_keys.key: text file with node IDs and topologies
complete_q_scores.key: text file with node IDs multiplied q scores
EN_node_vals.key: text file with node IDs and EN values
create_pie_charts_tree.py: script needed to visualize the tree with pie charts, pp1, and EN values plotted at nodes
ASTRAL_species_tree_full_annotation.newick: the species tree with full annotation from the ASTRAL analysis.
NOTE: It may be more useful to examine individual value files if you want to visualize the tree,
e.g., in figtree, since the full annotations are extensive and can make viewing difficult.

Complete_NT_concatenated_alignment.phy: the nucleotide alignment that includes unmodified third codon positions. The alignment is in phylip format.
Complete_NT_raxml_partitions.txt: the raxml-style partition file of the nucleotide partitions
Complete_NT_concatenated_tree.newick: the best maximum likelihood tree from the concatenated complete analysis NT with bootstrap values in newick format
Complete_NT_partitioned_tree.newick: the best maximum likelihood tree from the partitioned complete NT analysis with bootstrap values in newick format

Degeneracy_coded_nt_concatenated_alignment.phy: the degeneracy coded nucleotide alignment in phylip format
Degeneracy_coded_nt_raxml_partitions.txt: the raxml-style partition file for the degeneracy coded nucleotide alignment
Degeneracy_coded_nt_concatenated_tree.newick: the best maximum likelihood tree from the degeneracy-coded concatenated analysis with bootstrap values in newick format
Degeneracy_coded_nt_partitioned_tree.newick: the best maximum likelihood tree from the degeneracy-coded partitioned analysis with bootstrap values in newick format

count_ingroup_taxa.py: script that counts the number of ingroup and/or outgroup taxa present in an alignment