Phylogenomic analyses data of the avian phylogenomics project.

Dataset type: Genomic
Data released on November 27, 2014

Determining the evolutionary relationships of modern birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neoagnathae and two of the five Palaegnoathae orders, and used the genomes to construct various genome-scale avian phylogenetic trees and perform comparative genomics analyses.
Here we release the datasets associated with the phylogenomic analyses, which include genome scale alignments, gene tree files (including binned supergene trees), species tree files (including timetrees), and loci sequence files including nucleotide, amino acid, indels, and transposable elements. We hope that this resource will serve future efforts in phylogenomics, evolutionary biology, and trait analyses.

Additional details

Read the peer-reviewed publication(s):

Zhang, G., Li, B., Li, C., Gilbert, M. T. P., Jarvis, E. D., & Wang, J. (2014). Comparative genomic data of the Avian Phylogenomics Project. GigaScience, 3(1). doi:10.1186/2047-217x-3-26
Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … Meredith, R. W. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. doi:10.1126/science.1251385
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … Howard, J. T. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320–1331. doi:10.1126/science.1253451

Related datasets:

doi:10.5524/101041 Continues doi:10.5524/101000

File NameSample IDData TypeFile FormatSizeRelease Date 
AlignmentsTAR4.28 GB2014-12-11
AlignmentsTAR3.85 GB2014-12-11
AlignmentsTAR2.34 GB2014-12-11
Phylogenetic treeTAR226.06 MB2014-12-11
ReadmeTEXT10.77 KB2014-12-11
OtherTAR20.02 KB2014-12-11
Tabular dataTAR1.81 KB2014-12-11
Displaying 1-7 of 7 File(s).
Date Action
October 13, 2015 File All.aln.gz updated
October 17, 2015 File Newick_tree_files.tar.gz updated
October 17, 2015 File All.aln.gz updated
October 17, 2015 File Concatenated_alignments.tar.gz updated
October 17, 2015 File FASTA_files_of_loci_datasets.tar.gz updated
October 17, 2015 File readme.txt updated
October 17, 2015 File Scripts.tar.gz updated
October 17, 2015 File Transposable_elements.tar.gz updated
November 3, 2015 File Newick_tree_files.tar.gz updated
November 3, 2015 File Newick_tree_files.tar.gz updated