Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

Supplementary data for "Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny."
hamstrsearch_model_taxa.sh: Commands used to process translated transcriptomes and predicted proteins from genomes with the HaMStR orthology inference software.
HaMStR_v13_modelorganisms_concatenate_orthologs.sh: Script used to create single fasta files for each HaMStR orthogroup from "fa_dir" folders created by HaMStR.

Phylogenomic_workflow_data_and_script_used.zip:
The script orthology_script.sh contains the commands used to go from the output of HaMStR_v13_modelorganisms_concatenate_orthologs.sh to the results in the PhyloTreePruner "pruned" folder. The results of SCaFoS analysis are in /scafos/.
18S_rDNA_alignment.phy:Alignment corresponding to Figure S2.
Transcriptome_assemblies_and_translations.zip:Newly sequenced transcriptome assemblies generated using Trinity and translations generated using TransDecoder.