Lessons from assembling UCEs: a comparison of common methods and the case of Clavinomia (Halictidae)

This readme.txt file was generated on 2023-NOV-29 by Silas BossertThis repository contains supplementary files associated with the research article:Lessons from assembling UCEs: a comparison of common methods and the case of Clavinomia (Halictidae)by Silas Bossert, Alain Pauly, Bryan N. Danforth, Michael C. Orr, and Elizabeth A. MurrayFor questions and/or concerns please contact the lead author of the paper under silas.bossert [at] wsu.eduThis repository consists of 15 files.###1. 01_Supplemental_Information.pdf###This Pdf file contains supplementary information to the main article. The file is the same as the one provided on the website of the journal.###2. 02_Assembly_Comparisons.xlsx###This spreadsheet contains raw data on alignment and UCE statistics of the examined and compared UCE data sets.###3. 03_Distances_genetrees_speciestrees.R###This is an R script which was developed to efficiently compute phylogenetic distances between individual gene trees and a given refernce tree, even if the gene tree has incomplete taxon sampling. The R script is annoated; if questions arise, please contact the corresponding author.###4. 04_Beastfile_1.xml###The input file for the Beast analyses.###5. 05_Beast_chronogram.tre###The chronogram, which was estimated with Beast.###6. 06_Gene_trees.tar.gz###An archive which contains all individual gene trees estimated in the study.###7. 07_Species_trees.tar.gz###An archive which contains all species trees estimated in the present study, except for the Beast chronogram, which is provided as a separate file.###8. 08_Alignments_63_taxa.tar.gz###The alignments for the 63 taxon sets derived from assemblies of all five assemblers used in the present study (ABySS, HybPiper, SPAdes, Trinity, Velvet).###9. 09_Alignments_75_taxa.tar.gz###The alignments for the 75 taxon sets derived from assemblies of all five assemblers used in the present study (ABySS, HybPiper, SPAdes, Trinity, Velvet).###10. 10_Assemblies_Abyss.rar###The assembled, contiguous sequences which were generated with the ABySS assembly software.###1. 11_Assemblies_HybPiper.rar###The assembled, contiguous sequences which were generated with the HybPiper pipeline.###12. 12_Assemblies_SPAdes.rar###The assembled, contiguous sequences which were generated with the SPAdes assembly software.###13. 13_Assemblies_Trinity.rar###The assembled, contiguous sequences which were generated with the Trinity assembly software.###14. 14_Assemblies_Velvet.rar###The assembled, contiguous sequences which were generated with the Velvet assembly software.###15. 15_Other_Assemblies.rar###This archive contains 12 additional assembly files which were derived from other studies. See the Supplementary Information or the main article for details on the assemblies.