This is the public archive with ID 341f72708302f1d0c461ad616e783b86 created on 2024-03-10 13:39:55 by Josefin Stiller, BIO <josefin.stiller@bio.ku.dk>.
Archive Meta Data
Author(s)
Josefin Stiller, Siavash Mirarab, Guojie Zhang
Title
Data repository for Stiller et al. Nature 2024
Description
This repository contains the data accompanying manuscript "Complexity of avian evolution revealed by family-level genomes" in Nature by Josefin Stiller, Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González, David A. Duchêne, Qi Fang, Yuan Deng, Alexey Kozlov, Alexandros Stamatakis, Santiago Claramunt, Jacqueline M. T. Nguyen, Simon Y. W. Ho, Brant C. Faircloth, Julia Haag, Peter Houde, Joel Cracraft, Metin Balaban, Uyen Mai, Guangji Chen, Rongsheng Gao, Chengran Zhou, Yulong Xie, Zijian Huang, Zhen Cao, Zhi Yan, Huw A. Ogilvie, Luay Nakhleh, Bent Lindow, Benoit Morel, Jon Fjeldså, Peter A. Hosner, Rute R. da Fonseca, Bent Petersen, Joseph A. Tobias, Tamás Székely, Jonathan David Kennedy, Andrew Hart Reeve, Andras Liker, Martin Stervander, Agostinho Antunes, Dieter Thomas Tietze, Mads Bertelsen, Fumin Lei, Carsten Rahbek, Gary R. Graves, Mikkel H. Schierup, Tandy Warnow, Edward L. Braun, M. Thomas P. Gilbert, Erich D. Jarvis, Siavash Mirarab, Guojie Zhang. The deposited data can be either accessed through a graphical user interface or using the command line. Command line links are given for individual files or for batch download of large numbers of files in the README.txt. The repository contains 8 main directories (some with subdirectories marked *): 01) Alignments and gene trees * Intergenic regions * Exons * Introns * UCEs * Total evidence datasets * Whole genome alignment in 10kb windows 02) Characteristics of alignments and gene trees * Locus Mastertable * GC content * Phylogenetic model adequacy 03) Species trees 04) Time trees 05) Subsetting experiments 06) Polytomy test 07) Scripts to reproduce figures 08) Supplementary results
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