Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera

Branstetter MG, Longino JT, Ward PS, Faircloth BC

Date Published: February 14, 2017

DOI: http://dx.doi.org/10.5061/dryad.89n87

 

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Title Raw Illumina reads (SRA PRJNA360290).
Description Raw Illumina reads for all enriched samples included in this study. Data available from the NCBI Sequence Read Archive using BioProject accession PRJNA360290.
Download ../bioproject/?term=PRJNA360290 (0 bytes)
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Title Alignment supermatrices and data partitioning files
Downloaded 45 times
Description Alignment supermatrices and associated data partitioning files for all analyses performed in this study. Includes 101-sample and 1060-sample data sets. Includes PartitionFinder configuration file for hcluster analysis of UCE loci.
Download alignment-supermatrices-&-partitioning-files.zip (76.20 Mb)
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Title Tables and table captions - Excel
Downloaded 19 times
Description All tables and table captions from the main text and supporting information of this study. Provided in Excel format.
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Title Appendix 2 from study.
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Description Appendix 2 from study. Includes supplementary methods, table captions, figures, and references.
Download appendix2-supporting-information-methods-t....docx (270.7 Kb)
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Title Exon and rDNA alignments (trimmed) - enriched samples only.
Downloaded 8 times
Description Exon and rDNA alignments for all enriched samples included in this study. Alignments trimmed to remove introns and excessive flanking DNA.
Download exon-rDNA-alignments-trimmed-enriched-tax...ly.zip (185.4 Kb)
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Title Exon and rDNA alignments (untrimmed) - enriched samples only.
Downloaded 8 times
Description Exon and rDNA alignments for all enriched samples included in this study. Alignments untrimmed.
Download exon-rDNA-alignments-untrimmed-enriched-t...ly.zip (622.8 Kb)
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Title Hym-v2 bait set files.
Downloaded 29 times
Description Hymenoptera v2 bait set files. Includes the principal and ant-specific UCE bait set files, and the ant-exon bait set files.
Download hym-v2-bait-set-files-complete.zip (2.198 Mb)
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Title Phylogenetic trees.
Downloaded 18 times
Description All phylogenetic trees from study in PDF and either Newick or Nexus formats. Includes 101-terminal and 1060-terminal trees.
Download phylogenetic-trees.zip (388.9 Kb)
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Title R script to calculate locus stats.
Downloaded 9 times
Description R script used to calculate mean gene-tree bootstrap and mean GC-variance among taxa for a given set of gene trees and associated alignment files.
Download r-script-for-locus-stats.r (3.038 Kb)
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Title UCE contigs - aligned, trimmed, and filtered (Ants101T-F90).
Downloaded 15 times
Description All UCE contigs (aligned and trimmed) for the Ants101T-F90 data set. Contigs aligned with MAFFT and trimmed with Gblocks. Alignments filtered to include only those alignments with at least 90% taxon occupancy.
Download uce-contigs-aligned-gblocks-trimmed-taxon...90.zip (19.00 Mb)
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Title All UCE contigs - aligned, untrimmed.
Downloaded 13 times
Description All UCE contigs from enriched taxa. Data aligned, but not trimmed or filtered for taxon occupancy. Data also available from GenBank using BioProject accession PRJNA360290.
Download uce-contigs-aligned-untrimmed-unfiltered.zip (105.5 Mb)
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Title UCE contigs from genome-enabled taxa.
Downloaded 12 times
Description UCE contigs extracted from genome-enabled taxa and used in some analyses. Files can be used to add genome-enabled taxa to UCE data sets. Contigs include UCE core region and 700 bp of flanking DNA.
Download uce-contigs-for-genome-enabled-taxa.zip (91.07 Mb)
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When using this data, please cite the original publication:

Branstetter MG, Longino JT, Ward PS, Faircloth BC (2017) Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera. Methods in Ecology and Evolution 8(6): 768-776. http://dx.doi.org/10.1111/2041-210x.12742

Additionally, please cite the Dryad data package:

Branstetter MG, Longino JT, Ward PS, Faircloth BC (2017) Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.89n87
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