Astral analysis files for the 75% (75p) complete data set.

UCEs Fasta file

Lemmon-etal2012_Phylogenetics_BEST_Amniote_treeDist

Accession numbers for raw-reads in NCBI SRA.

Lemmon-etal2012_Phylogenetics_BEST_Tetrapod

Nexus files of all target capture UCE sequences used in this study.

NOTES describing the pipeline steps used to analyze the ABYSS data.

UCEs Fasta file

This Excel file contains all of the supplemental tables and table captions.

Nexus file containing sequences for 19 whole mitochondrial genomes and a MrBayes block with MrBayes settings.

Overall description of files/project with additional information on code used, SRA accessions, etc.

Steps used during the phylogenetic analysis. All used the PHYLUCE software package (available from: https://github.com/faircloth-lab/phyluce).

Output of one replicate of *BEAST species tree analyses for the UCE dataset. Three .trees files for the three UCE datasets: complete, only including 10 or more parsimony...

Data files and scripts for all biogeography, trait, and diversification rate analyses.

All supplementary tables (same as Appendix 1 in paper).

Dataset 6 (shallow_flanks). Nexus file containing 749 loci and 35 taxa. The Extract_probe_region.py script was used on Dataset 4 to isolate data coming from the flanking regions...

The file "Scripts - readme.txt" explains which MATLAB scripts are the main files and how the parameters in the header need to be set to obtain the diagrams in the paper, based...

Lemmon-etal2012_Phylogenetics_BEST_Tetrapod_treeDist

UCEs Fasta file

Top level file defining taxon sets used in analyses (e.g. ABYSS and TRINITY, with and without sawflies.