Data from: Building the avian tree of life using a large-scale, sparse supermatrix

Burleigh JG, Kimball RT, Braun EL

Date Published: January 6, 2015

DOI: http://dx.doi.org/10.5061/dryad.r6b87

 

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Title SupplementalFigure1
Downloaded 59 times
Description PDF figure describing relationships among Passeriformes families. Each clade that contained species from a single family was collapsed to a single terminal. Italics indicate families that were not monophyletic. The number in parentheses after the family names indicates the number of species in the full tree represented by the lineage. ML bootstrap support values are presented above branches; “*” indicates 100% bootstrap support. Support values on terminal branches indicate the support for monophyly of specific families.
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Title AllBird.NewNames.7000Taxa.phy
Downloaded 38 times
Description Alignment of the entire 7000-taxon supermatrix in Phylip Format. This alignment uses the revised Clements names instead of the original GenBank names, and taxon names include the orders and families.
Download AllBird.NewNames.7000Taxa.phy.gz (10.76 Mb)
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Title GeneBorders
Downloaded 19 times
Description This file indicates the starting and ending alignment positions for each gene in the supermatrix.
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Title TotalAccessionTable
Downloaded 56 times
Description Tab-delimited text file that includes the Genbank ID numbers for all of the sequences in the supermatrix. The first column has the Clements names and the second has the original GenBank names. The other columns have the accession numbers for a specified gene.
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Title BigBird.All.NewNames.7000Taxa.tre
Downloaded 29 times
Description Newick strings of the maximum likelihood (ML) and ML bootstrap trees built from the original supermatrix. The first tree in the file is the ML tree, and the other 100 trees are ML bootstrap trees. The numbers represent molecular branch lengths.
Download BigBird.All.NewNames.7000Taxa.tre.gz (22.35 Mb)
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Title BigBird.All.NewNames.6714Taxa.tre
Downloaded 36 times
Description Neiwck strings of the maximum likelihood (ML) and ML bootstrap trees built from the original supermatrix, trimmed to only have one representative taxon per species and edited to correspond to the Clements taxonomy. These are subtrees of “BigBird.All.NewNames.7000Taxa.tre”. The first tree in the file is the ML tree, and the other 100 trees are ML bootstrap trees. The numbers represent molecular branch lengths.
Download BigBird.All.NewNames.6714Taxa.tre.gz (21.42 Mb)
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When using this data, please cite the original publication:

Burleigh JG, Kimball RT, Braun EL (2014) Building the avian tree of life using a large-scale, sparse supermatrix. Molecular Phylogenetics and Evolution 84: 53-63. http://dx.doi.org/10.1016/j.ympev.2014.12.003

Additionally, please cite the Dryad data package:

Burleigh JG, Kimball RT, Braun EL (2014) Data from: Building the avian tree of life using a large-scale, sparse supermatrix. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r6b87
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