Data from: A framework phylogeny of the American oak clade based on sequenced RAD data

Hipp AL, Eaton DAR, Cavender-Bares J, Fitzek E, Nipper R, Manos PS

Date Published: April 25, 2014

DOI: http://dx.doi.org/10.5061/dryad.ts2hj

 

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Title pyRAD output: c88_d6m4p2_wRE.readloci
Downloaded 56 times
Description Locus file from pyRAD, clustering at 0.88 similarity, a minimum of 4 individuals per locus. This file can be read in using the read.pyRAD function of the R package RADami (http://cran.r-project.org/web/packages/RADami/index.html); structure of the data is described in the documentation to pyRAD (code.google.com/p/pyrad/; www.dereneaton.com/software). Briefly, each locus is represented by a sequence alignment of those individuals for which the cluster was found, and loci are delimited by a break line that indicates variable sites.
Download c88_d6m4p2_wRE.readloci.zip (5.469 Mb)
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Title pyRAD loci output: c88_d6m10p2_wRE.readloci
Downloaded 62 times
Description Locus file from pyRAD, clustering at 0.88 similarity, a minimum of 10 individuals per locus. This file can be read in using the read.pyRAD function of the R package RADami (http://cran.r-project.org/web/packages/RADami/index.html); structure of the data is described in the documentation to pyRAD (code.google.com/p/pyrad/; www.dereneaton.com/software). Briefly, each locus is represented by a sequence alignment of those individuals for which the cluster was found, and loci are delimited by a break line that indicates variable sites.
Download c88_d6m10p2_wRE.readloci.zip (3.214 Mb)
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Title Phylip file: d6m10.phy
Downloaded 48 times
Description Phylip-style (sequential) multiple alignment file, generated from pyRAD loci d6m10 file.
Download d6m10.phy.zip (8.060 Mb)
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Title blast2go results: 2013-04-09.data
Downloaded 35 times
Description blast2go results of d6m10 loci against three EST databases.
Download 2013-04-09.data.zip (1.960 Mb)
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Title Phylogenetic analyses.EST.2013-03-28
Downloaded 38 times
Description Results of phylogenetic analyses conducted on EST-length subsets of the original RAD dataset.
Download analyses.EST.2013-03-28.zip (270.6 Mb)
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Title BLASTN results: blasts.2013-02-21
Downloaded 35 times
Description BLASTN results of m10 RAD locus consensus sequences against EST databases in NCBI.
Download blasts.2013-02-21.zip (1.333 Mb)
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Title R source file: PLOS.2013.analyses
Downloaded 51 times
Description R source file for performing analyses presented in the paper that were not ported to RADami.
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Title R source: PLOS.2013.blast2go
Downloaded 28 times
Description R code for checking and summarizing blast2go results presented in paper.
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When using this data, please cite the original publication:

Hipp AL, Eaton DAR, Cavender-Bares J, Fitzek E, Nipper R, Manos PS (2014) A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS ONE 9(4): e93975. http://dx.doi.org/10.1371/journal.pone.0093975

Additionally, please cite the Dryad data package:

Hipp AL, Eaton DAR, Cavender-Bares J, Fitzek E, Nipper R, Manos PS (2014) Data from: A framework phylogeny of the American oak clade based on sequenced RAD data. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ts2hj
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