<b>Lessons from assembling UCEs: a comparison of common methods and the case of </b><b><i>Clavinomia </i></b><b>(Halictidae)</b>

This readme.txt file was generated on 2023-NOV-29 by Silas Bossert This 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.edu This 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.