Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

García N, Folk RA, Meerow AW, Chamala S, Gitzendanner MA, Oliveira RSd, Soltis DE, Soltis PS

Date Published: April 11, 2017

DOI: http://dx.doi.org/10.5061/dryad.kg686

 

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Title bait-120-60-selection
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Description Sequences used to design MYbaits kit.
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Title Curated alignments and gene trees
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Description Includes alignments and partition files, RAxML bootstrap and best tree files for curated nuclear loci.
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Title aTRAM alignments and gene trees
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Description Includes raw alignments for 48 nuclear loci obtained through aTRAM assembly. Also edited alignments and RAxML output files for 39 nuclear loci.
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Title Concatenated alignments and trees
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Description Includes alignments and trees for concatenated analyses of 39 aTRAM nuclear loci, 15 curated nuclear loci (including and excluding noncoding regions), and curated nuclear plus plastid regions.
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Title Networks
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Description Includes tree and nexus files used to compute neighbor-net and hybridization networks.
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Title ASTRAL
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Description Includes output files from ASTRAL-II analyses of 12 curated nuclear loci and 39 aTRAM nuclear loci.
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Title BUCKy
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Description Includes alignments used in BUCKy and output files for analyses with two different alpha values (1, INFINITY).
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Title *BEAST
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Description Includes xml, log, and species tree files for all runs performed for each analysis.
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Title JML
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Description Includes control and output files for JML analyses of 12 curated nuclear loci and plastid coding sequences. Also collection of *BEAST species trees used in analyses.
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Title Coalescent simulations
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Description Includes simulated gene trees under three branch length scaling factors from ASTRAL species trees inferred from 12 curated loci and 39 aTRAM loci.
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Title run_cut_trim_blat.qsub
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Description Submission script to run Cutadapt, Sickle, Blat, and python script to pull out blat hits.
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Title get_reads_w_blat_hit_pe
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Description Python script
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Title Reference sequences
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Description Transcriptomic reference sequences for 48 nuclear loci.
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When using this data, please cite the original publication:

García N, Folk RA, Meerow AW, Chamala S, Gitzendanner MA, Oliveira RSd, Soltis DE, Soltis PS (2017) Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Molecular Phylogenetics and Evolution 111: 231–247. http://dx.doi.org/10.1016/j.ympev.2017.04.003

Additionally, please cite the Dryad data package:

García N, Folk RA, Meerow AW, Chamala S, Gitzendanner MA, Oliveira RSd, Soltis DE, Soltis PS (2017) Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.kg686
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