Data from: Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources

Kieran TJ, Gordon ERL, Forthman M, Hoey-Chamberlain R, Kimball RT, Faircloth BC, Weirauch C, Glenn TC

Date Published: October 30, 2018

DOI: https://doi.org/10.5061/dryad.425vg4m

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title scripts
Downloaded 1 time
Description Zip file of scripts used in PHYLUCE pipeline from assembly through RAxML trees. Scripts include those for the "empirical" data set and those for the "empirical + in silico" data set with the extension "_empIns added to each script name.
Download scripts.zip (14.70 Kb)
Details View File Details
Title config_files
Downloaded 1 time
Description Zip file of configuration files used in the PHYLUCE pipeline. Files included for assembly, Illuminiprocessor, taxonomic sets, and incomplete matrix. Taxon-set2.conf and all_empIns-taxa-incomplete.conf are for the "empirical + in silico" data sets.
Download config_files.zip (20.94 Kb)
Details View File Details
Title UCE_loci
Description Zip of .fasta and .incomplete files of UCE loci identified. Output from extract_fasta.sh and extract_fasta_empIns.sh scripts. Used as input for internal_trim.sh and internal_trim_empIns.sh scripts respectively.
Download UCE_loci.zip (17.90 Mb)
Details View File Details
Title RAxML_alignment_input_&_Trees_output
Description Zip of UCE loci and character set files used as input for RAxML for both the "empirical" and "empirical + in silico" (empIns) data sets for the 60% data matrix. The output reconciled tree from RAxML for each data set.
Download RAxML_alignInput_&_Trees.zip (894.9 Kb)
Details View File Details
Title phyluce_workflow
Downloaded 2 times
Description Text file of script usage workflow of the analyses performed in PHYLUCE and RAxML.
Download phyluce_workflow.txt (922 bytes)
Details View File Details
Title UCE_alignments
Description Zip of individual UCE loci alignments from MAFFT in nexus format, output of internal_trim.sh and internal_trim_empIns.sh scripts, for input into Gblocks.
Download UCE_alignments.zip (24.11 Mb)
Details View File Details

When using this data, please cite the original publication:

Kieran TJ, Gordon ER, Forthman M, Hoey-Chamberlain R, Kimball RT, Faircloth BC, Weirauch C, Glenn TC (2019) Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources. Molecular Phylogenetics and Evolution 130: 297-303. https://doi.org/10.1016/j.ympev.2018.10.026

Additionally, please cite the Dryad data package:

Kieran TJ, Gordon ERL, Forthman M, Hoey-Chamberlain R, Kimball RT, Faircloth BC, Weirauch C, Glenn TC (2019) Data from: Insight from an ultraconserved element bait set designed for hemipteran phylogenetics integrated with genomic resources. Dryad Digital Repository. https://doi.org/10.5061/dryad.425vg4m
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: