Data from: Comparison of target-capture and restriction-site associated DNA sequencing for phylogenomics: a test in cardinalid tanagers (Aves, genus: Piranga)

Manthey JD, Campillo LC, Burns KJ, Moyle RG

Date Published: January 26, 2016

DOI: http://dx.doi.org/10.5061/dryad.j5n06

 

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Title piranga_snps.structure
Downloaded 15 times
Description SNPs from restriction-site associated DNA sequencing in STRUCTURE format.
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Title uce_nexus
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Description Nexus files of all target capture UCE sequences used in this study.
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Title uce_beast
Downloaded 53 times
Description Output of one replicate of *BEAST species tree analyses for the UCE dataset. Three .trees files for the three UCE datasets: complete, only including 10 or more parsimony informative sites, and only including 20 or more parsimony informative sites.
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Title uce_phyml
Downloaded 12 times
Description Results of species tree analyses (both bootstraps and summarized tree) using PhyML gene trees as input. Output is shown for three UCE datasets, including all 734 loci, only loci with 10 or more parsimony informative sites, and only loci with 20 or more parsimony informative sites.
Download uce_phyml.zip (105.4 Kb)
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Title uce_raxml
Downloaded 23 times
Description Results of species tree analyses (both bootstraps and summarized tree) using RAxML gene trees as input. Output is shown for three UCE datasets, including all 734 loci, only loci with 10 or more parsimony informative sites, and only loci with 20 or more parsimony informative sites.
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Title uce_beast_input
Downloaded 22 times
Description Input files for *BEAST with each of the three UCE datasets, including all loci, only those with 10 or more parsimony informative sites (PI), and only loci with 20 or more PI sites.
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Title rad_snapp_trees
Downloaded 26 times
Description Output of two runs of SNAPP using the RAD-seq SNP data.
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Title rad_species_input
Downloaded 23 times
Description Input nexus files from the RAD-seq dataset for SNAPP and SVDquartets.
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Title Piranga Trees
Downloaded 54 times
Description Pictures of species trees for all RAD-seq and UCE analyses used in this study. Descriptions in the PDF.
Download Piranga_Supp_Info.pdf (1.664 Mb)
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Title multilocus_bootstraps
Downloaded 17 times
Description Multilocus bootstraps for each dataset (734 loci, 10 PI dataset, and 20PI dataset) using either PhyML or RAxML.
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Title piranga_supp_table
Downloaded 31 times
Description Summary information and statistics for each sample, including barcodes used for RAD sequencing, number of RAD tags, coverage of RAD loci, adapters used in UCE library prep, UCE sequencing coverage, number of recovered UCEs, and length of UCEs.
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Title piranga_uce_snapp
Downloaded 21 times
Description Files associated with SNAPP analysis of UCE SNPs. Input nexus file, and output of two SNAPP runs. Output includes posterior sampling of all trees (.trees files), tree summaries (.tre) and pictures of the output trees (.pdf).
Download piranga_uce_snapp.zip (2.977 Mb)
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When using this data, please cite the original publication:

Manthey JD, Campillo LC, Burns KJ, Moyle RG (2016) Comparison of target-capture and restriction-site associated DNA sequencing for phylogenomics: a test in cardinalid tanagers (Aves, genus: Piranga). Systematic Biology 65(4): 640-650. http://dx.doi.org/10.1093/sysbio/syw005

Additionally, please cite the Dryad data package:

Manthey JD, Campillo LC, Burns KJ, Moyle RG (2016) Data from: Comparison of target-capture and restriction-site associated DNA sequencing for phylogenomics: a test in cardinalid tanagers (Aves, genus: Piranga). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.j5n06
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