Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

Faircloth BC, Branstetter MG, White ND, Brady SG

Date Published: September 19, 2014

DOI: http://dx.doi.org/10.5061/dryad.46195

 

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Title hymenoptera-uce-probes.fasta
Downloaded 66 times
Description FASTA file containing target enrichment bait sequences for UCE loci in hymenoptera.
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Title in-silico-NOTES
Downloaded 68 times
Description NOTES describing the pipeline steps used to analyze the in silico data.
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Title in-silico-contigs.tar.gz
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Description UCE contigs sliced from available hymenopteran genomes.
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Title in-silico-uce-probes-to-contigs.lastz.tar.gz
Downloaded 16 times
Description LASTZ files showing mapping of UCE probes onto in silico genome slices AND probe.matches.sqlite database.
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Title in-silico-taxon-set-alignment-data.tar.gz
Downloaded 37 times
Description Archive file containing nested directories of in-silico alignment and analysis data. See overall README or file-specific README.
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Title hymenoptera-data-sets.conf
Downloaded 30 times
Description Top level file defining taxon sets used in analyses (e.g. ABYSS and TRINITY, with and without sawflies.
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Title abyss-NOTES
Downloaded 37 times
Description NOTES describing the pipeline steps used to analyze the ABYSS data.
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Title abyss-contigs.tar.gz
Downloaded 17 times
Description UCE contigs enriched from hymenopteran taxa and assembled using ABySS.
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Title abyss-uce-probes-to-contigs.lastz.tar.gz
Downloaded 20 times
Description LASTZ files showing mapping of UCE probes onto in ABySS contigs AND probe.matches.sqlite database.
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Title abyss-probe-alignment-logs.tar.gz
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Description Log files from ABySS probe alignment.
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Title abyss-taxon-set-alignment-data.tar.gz
Downloaded 31 times
Description Archive file containing nested directories of ABySS alignment and analysis data. See overall README or file-specific README.
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Title trinity-NOTES
Downloaded 63 times
Description NOTES describing the pipeline steps used to analyze the TRINITY data.
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Title trinity-contigs.tar.gz
Downloaded 17 times
Description UCE contigs enriched from hymenopteran taxa and assembled using TRINITY.
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Title trinity-uce-probes-to-contigs.lastz.tar.gz
Downloaded 10 times
Description LASTZ files showing mapping of UCE probes onto TRINITY contigs AND probe.matches.sqlite database.
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Title trinity-assembly-and-probe-alignment-logs.tar.gz
Downloaded 11 times
Description Log files from TRINITY probe alignment.
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Title trinity-taxon-set-alignment-data.tar.gz
Downloaded 49 times
Description Archive file containing nested directories of TRINITY alignment and analysis data. See overall README or file-specific README.
Download trinity-taxon-set-alignment-data.tar.gz (264.2 Mb)
Download README.txt (4.193 Kb)
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Title in-silico-RENAMED-TIPS.tree
Downloaded 8 times
Description In silico tree with tips renamed to full species binomial.
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Title abyss-WITH-SAWFLIES-100-bootrep-RENAMED-TIPS.tree
Downloaded 7 times
Description ABySS (with sawfly taxa) tree with tips renamed to full species binomial.
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Title trinity-WITH-SAWFLIES-100-bootrep-RENAMED-TIPS.tree
Downloaded 9 times
Description Trinity (with sawfly taxa) tree with tips renamed to full species binomial.
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Title trinity-WITHOUT-SAWFLIES-100-bootrep-RENAMED-TIPS.tree
Downloaded 7 times
Description Trinity (*without* sawfly taxa) tree with tips renamed to full species binomial.
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Title Tables.xlsx
Downloaded 36 times
Description Excel file of tables in manuscript.
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Title figure-1-hymenoptera-with-sawflies
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Description Illustrator file of Figure 1, sources of Figure 1 images, and an archive of photoshop cartoon images used in Figure 1 are located in figshare at doi:10.6084/m9.figshare.1173286
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Title supplemental-figures.tar.gz
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Description Archive of supplemental figures (Illustrator documents).
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Title pycogent-distance-estimates.xlsx
Downloaded 42 times
Description Distances estimates output by PyCogent as xlsx file.
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Title r-steps-and-data.tar.gz
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Description Steps and data used in R for barplots and glms.
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Title README
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Description Overall description of files/project with additional information on code used, SRA accessions, etc.
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When using this data, please cite the original publication:

Faircloth BC, Branstetter MG, White ND, Brady SG (2015) Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Molecular Ecology Resources 15(3): 489-501. http://dx.doi.org/10.1111/1755-0998.12328

Additionally, please cite the Dryad data package:

Faircloth BC, Branstetter MG, White ND, Brady SG (2014) Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.46195
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