Alignments

Data Available for Download

Datasets used in publications produced by the Early Bird group are available for download. Specific datasets include:

  • Data from Hackett, Kimball, Reddy, and 15 additional co-authors (2008) Science, 320: 1763-1768. [list of files for download]
  • Data from Harshman, E. Braun, M. Braun, and 14 additional co-authors (2008) PNAS, 105: 13462-13467.  [list of files for download]
  • Data matrices used for analyses of the gamebird (order Galliformes) tree of life, including those from: [list of files for download]
    • Cox et al. (2007) Auk 124: 71-84.
    • Kimball and Braun (2008) J Avian Biology, 39:  438-445.
    • Bonilla et al. (2010) MPE 56: 536-542.
    • Kimball et al. (2011) Int J Evol Biol Article ID 423938.
  • Data on TE (transposable element) insertions in the Hackett et al. (2008) data, compiled by Han et al. (2011) [list of files for download]
  • Data matrices from Yuri et al. (2013) Biology in press. These files correspond to gap characters coded from Hackett et al. [list of files for download]

Full information about these papers is available on the publications page.

Data from Hackett et al. 2008

A total of 19 gene regions were used to examine relationships among major avian lineages in Hackett et al. (2008):

  • 19 gene supermatrix in nexus format [download]
  • Alignments of individual gene regions. [ALDOB] [BDNF] [CLTC] [CRYAA] [EEF2] [EGR1] [FGB] [IRF2] [GH1] [HMGN2] [MB] [MUSK] [MYC] [NGF] [NTF3] [PCBD1] [RHO] [TGFB2] [TPM1] [COMING SOON]

Data from Harshman et al. 2008

A total of 20 gene regions were used to examine relationships among paleognaths (ratites and tinamous) in Harshman et al. (2008):

  • 20 gene supermatrix in nexus format [download]
  • Alignments of individual gene regions. [ALDOB] [BDNF] [CLTC] [CLTCL1] [CRYAA] [EEF2] [EGR1] [FGB] [IRF2] [GH1] [HMGN2] [MB] [MUSK] [MYC] [NGF] [NTF3] [PCBD1] [RHO] [TGFB2] [TPM1] [COMING SOON]

Rare Genomic Change Data

Files containing the binary coded RGC (rare genomic change) data are available. If you use these data please cite Hackett et al. (2008) as the source of the sequence data and the papers listed below for the specific analysis:

Data from analyses of Galliformes

The Kimball-Braun lab has paid particular attention to resolving relationships within the order Galliformes.  Data matrices from publications focused on this group are presented below:

Both the 6 gene supermatrix (4 nuclear introns and 2 mt coding regions) for 170 taxa and the trait matrix from Kimball et al. (2011)  [download nexus format alignment] [download nexus format trait data]