Data from: Phylogenomics from whole genome sequences using aTRAM

• Main Authors: 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.
• Other Authors: Federated Research Data Repository, Dépôt fédéré de données de recherche
• Format: Dataset
• Language: unknown
• Published: UBC Dataverse 2016
• Subjects: Other; Holocene; Genome sequencing; Bothriometopus macrocnemus; Antarctopthirus microchir; present day; Stimulopalpus japonicus; Haematopinus eurysternus; Hoplopleura arboricola; aTRAM; Proechinopthirus fluctus; Pediculus schaeffi; Pediculus humanus; Pthirus pubis; Linognathus spicatus; Pedicinus badii; Neohaematopinus pacificus; Pthirus gorillae; Degeeriella rufa; gene assembly; Osborniella crotophagae; Bureelia antiqua; Phylogenomics; Life sciences; medicine and health care; stat; envir; Antarc*
• Online Access: https://doi.org/10.5683/SP2/JQGMVL; https://doi.org/10.5061/dryad.26j38; https://doi.org/10.14288/1.0397756

Dryad version number: 1 Version status: submitted Dryad curation status: Published Sharing link: https://datadryad.org/stash/share/PR_oEYNZ-85sEFxTV9xmFYeC22Nk8_UTs1QalxMiACs Storage size: 8736762 Visibility: public Usage notes Concatenated alignment and tree 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. Dataset_1.zip Individual Gene Trees and Alignments 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. Dataset_2.zip SupplementaryTable DNA extraction, and quality clean up for each dataset. Illumina reads. Alignments of each gene and the tree analysis. Supplementary Figure 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. SupplementalFigure1.pdf 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 (<1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10−30×). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 ...