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