Phylogenomic analyses data of the avian phylogenomics project.
Dataset type: Genomic
Data released on November 27, 2014
Jarvis ED; Mirarab S; Aberer AJ; Houde P; Li C; Ho SYW; Faircloth BC; Nabholz B; Howard JT; Suh A; Weber CC; da Fonseca RR; Alfaro-Nunez A; Narula N; Liu L; Burt DW; Ellegren H; Edwards SV; Stamatakis A; Mindell DP; Cracraft J; Braun EL; Warnow T; Wang J; Gilbert MTP; Zhang G (2014): Phylogenomic analyses data of the avian phylogenomics project. GigaScience Database. https://doi.org/10.5524/101041
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). https://doi.org/10.1186/2047-217x-3-26
- Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., Ödeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., … Hu, H. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311–1320. https://doi.org/10.1126/science.1251385
- Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., Suh, A., Weber, C. C., da Fonseca, R. R., Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., … Zhang, G. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320–1331. https://doi.org/10.1126/science.1253451
Related datasets:
doi:10.5524/101041 Continues doi:10.5524/101000
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Table SettingsFile Name | Description | Sample ID | Data Type | File Format | Size | Release Date | File Attributes | Download |
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description of files available from GigaDB | Readme | TEXT | 11.03 kB | 2014-12-11 | ||||
These are the transposable elements of owl, as described in the GigaScience manuscript. | Tabular data | TAR | 1.85 kB | 2014-12-11 | ||||
A selection of scripts used in the generation of this dataset. | Other | TAR | 20.50 kB | 2014-12-11 | ||||
Gene tree files (including binned supergene trees) and species tree files (including timetrees). | Phylogenetic tree | TAR | 237.04 MB | 2014-12-11 | ||||
This archive includes filtered and unfiltered alignments of individual loci. | Alignments | TAR | 2.52 GB | 2014-12-11 | ||||
Contains the concatenated alignments that have been used in various ExaML and RAxML analyses. | Alignments | TAR | 4.13 GB | 2014-12-11 | ||||
Alignments used for all the ExaML concatenation analyses | Alignments | TAR | 4.60 GB | 2014-12-11 |
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 |