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18S_rDNA_alignment.phy (236.86 kB)
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Transcriptome_assemblies_and_translations.zip (130.52 MB)
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HaMStR_v13_modelorganisms_concatenate_orthologs.sh (0.58 kB)
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hamstrsearch_model_taxa.sh (21.38 kB)
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Phylogenomic_workflow_data_and_script_used.zip (225.35 MB)
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Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny
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modified on 2019-05-29, 23:08 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.
