Data from: Phylogenomics from whole genome sequences using aTRAM

Allen JM, Boyd B, Nguyen N, Vachaspati P, Warnow T, Huang DI, Grady PG, Bell KC, Cronk QCB, Mugisha L, Pittendrigh BR, Soledad Leonardi M, Reed DL, Johnson KP

Date Published: November 8, 2016

DOI: http://dx.doi.org/10.5061/dryad.26j38

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Concatenated alignment and tree
Downloaded 9 times
Description Alignment and phylogenetic tree of the concatenated 1,101 exon DNA alignment from 15 louse taxa. Genes were assembled from raw genomic DNA with aTRAM and exons extracted and stitched together. Third codon position was removed due to base composition bias, and tree build in RAxML.
Download Dataset_1.zip (4.380 Mb)
Details View File Details
Title Individual Gene Trees and Alignments
Downloaded 8 times
Description All 1,101 gene trees and alignments for the 15 taxon dataset. Each gene was aligned using PASTA and UPP for fragmentary sequences. Each gene tree was built using ASTRAL.
Download Dataset_2.zip (4.198 Mb)
Details View File Details
Title SupplementaryTable
Downloaded 39 times
Description DNA extraction, and quality clean up for each dataset. Illumina reads. Alignments of each gene and the tree analysis.
Download SupplementaryTable.pdf (120.1 Kb)
Details View File Details
Title Supplementary Figure
Downloaded 14 times
Description Box plot of the standard deviations away from mean for each codon position for each of the GTR rate parameters. The majorities of the extreme outliers fell above 10 standard deviations from the mean and were removed from the analysis.
Download SupplementalFigure1.pdf (9.154 Kb)
Details View File Details

When using this data, please cite the original publication:

Allen JM, Boyd B, Nguyen N, Vachaspati P, Warnow T, Huang DI, Grady PG, Bell KC, Cronk QCB, Mugisha L, Pittendrigh BR, Soledad Leonardi M, Reed DL, Johnson KP (2017) Phylogenomics from whole genome sequences using aTRAM. Systematic Biology, online in advance of print. http://dx.doi.org/10.1093/sysbio/syw105

Additionally, please cite the Dryad data package:

Allen JM, Boyd B, Nguyen N, Vachaspati P, Warnow T, Huang DI, Grady PG, Bell KC, Cronk QCB, Mugisha L, Pittendrigh BR, Soledad Leonardi M, Reed DL, Johnson KP (2016) Data from: Phylogenomics from whole genome sequences using aTRAM. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.26j38
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: