UBC Research Data

Data from: Phylogenomics from whole genome sequences using aTRAM Allen, Julie M.; Boyd, Bret; Nguyen, Nam-Phuong; Vachaspati, Pranjal; Warnow, Tandy; Huang, Daisie I.; Grady, Patrick G. S.; Bell, Kayce C.; Cronk, Quentin C.B.; Mugisha, Lawrence; Pittendrigh, Barry R.; Soledad Leonardi, M.; Reed, David L.; Johnson, Kevin P.

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Abstract
Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (; Usage notes
Concatenated alignment and treeAlignment 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.Dataset_1.zip
Individual Gene Trees and AlignmentsAll 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.Dataset_2.zip
SupplementaryTableDNA extraction, and quality clean up for each dataset. Illumina reads. Alignments of each gene and the tree analysis.Supplementary FigureBox 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.SupplementalFigure1.pdf

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