Data from: Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing

 

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Title Nexus_alignments
Downloaded 58 times
Description Nexus files of analyzed regions for 27 anonymous nuclear loci and 3 mitochondrial fragments
Download Nexus_alignments.zip (94.52 Kb)
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Title MrBayes gene tree results
Downloaded 63 times
Description Input files and consensus trees from MrBayes gene tree analyses.
Download MB.zip (467.4 Kb)
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Title BUCKy infiles and results
Downloaded 39 times
Description BUCKy infiles and results from Bayesian concordance analysis of 26 nuclear loci.
Download BUCKy-a01.zip (46.02 Mb)
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Title RAxML_26nucDNA
Downloaded 37 times
Description Infile and results from RAxML analysis of concatenated nuclear DNA (26 anonymous loci).
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Title RAxML_mtDNA-partitioned
Downloaded 41 times
Description Infile and results from analysis of 3 mitochondrial gene fragments.
Download RAxML_mtDNA-partitioned.zip (90.09 Kb)
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Title Starbeast analysis - 44 tips
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Description Starbeast xml file and results from species tree analysis with every individual as a tip.
Download SB-44taxa.zip (33.04 Mb)
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Title Starbeast Species Tree
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Description Starbeast xml file and results from species tree analysis.
Download SB-speciesTree.zip (15.54 Mb)
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Title Script for making infiles
Downloaded 16 times
Description Python script used for making infiles for RAxML, MrBayes, and *BEAST analyses. Input is a nexus file with a MrBayes block appended; output are infiles for: RAxML with randomly-chosen allele for nuclear loci, MrBayes files for gene tree analyses with either all alleles or randomly-chosen allele for heterozygotes; *BEAST files with either all alleles or randomly-chosen allele for heterozygotes.
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Title Illumina Read Data
Downloaded 198 times
Description Illumina MiSeq paired reads by individual for 44 individuals (40 Pseudacris, 2 Hyla cinerea, 2 Acris gryllus). IDs correspond to those in Table 1 of the publication.
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When using this data, please cite the original publication:

Barrow LN, Ralicki HF, Emme SA, Moriarty Lemmon E (2014) Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing. Molecular Phylogenetics and Evolution 75: 78–90. http://dx.doi.org/10.1016/j.ympev.2014.02.007

Additionally, please cite the Dryad data package:

Barrow LN, Ralicki HF, Emme SA, Moriarty Lemmon E (2014) Data from: Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.23rc0
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