Data from: Deep phylogenetic incongruence in the angiosperm clade Rosidae

Sun M, Soltis DE, Soltis PS, Zhu X, Burleigh JG, Chen Z

Date Published: November 20, 2014

DOI: http://dx.doi.org/10.5061/dryad.7sg58

 

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Title single-copy nuclear gene analysis
Downloaded 22 times
Description Collection of 8,445 potentially informative ortholog sets extracted from Lee at al. (2011) for single-copy nuclear gene analysis.
Download SingleCopyGenes From Lee et al. 2011 Data.rar (64.09 Mb)
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Title Multi-copy nuclear gene analysis
Downloaded 4 times
Description Collection of 3,748 gene family alignments from 22 plant taxa for multi-copy nuclear gene analysis.
Download MultiCopyGenes.rar (104.7 Mb)
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Title Analysis of multi-gene matrices from chloroplast, mitochondrial, and nuclear sequences
Downloaded 16 times
Description 1. Files from the 82-taxon, 78-gene cpDNA analysis. This compressed file includes: 82-taxon, 78-gene cpDNA nucleotide, AA, and RY-coding , and 1st & 2nd condon only alignments; associated AA tree, RY-coding tree,78 individual gene trees, and tree of 78-gene 1st & 2nd condon positions only; trees and sorted matrices from method to remove highly variable sites. 2. Files from the 79-taxon, 4-gene mtDNA analysis. This compressed file includes: 79-taxon, 4-gene mtDNA nucleotide, AA, RY-coding and 1st & 2nd condon only alignments; associated AA tree, RY-coding tree, 4 individual gene trees, and tree of 4-gene 1st & 2nd condon positions only; trees and sorting matrices method to remove highly variable sites. 3. Files from the 92-taxon, 5-gene nuDNA analysis. This compressed file includes: 92-taxon, 5-gene nuDNA nucleotide, AA, RY-coding, and 1st & 2nd condon only alignments; associated AA tree, RY-coding tree, 5 individual gene trees, and tree of 5-gene 1st & 2nd condon positions only; sorting matrices and trees from method to remove highly variable sites.
Download README.txt (2.103 Kb)
Download Analysis of multi-gene matrices CP_MT_NU_...ed.rar (19.17 Mb)
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When using this data, please cite the original publication:

Sun M, Soltis DE, Soltis PS, Zhu X, Burleigh JG, Chen Z (2014) Deep phylogenetic incongruence in the angiosperm clade Rosidae. Molecular Phylogenetics and Evolution 83: 156-166. http://dx.doi.org/10.1016/j.ympev.2014.11.003

Additionally, please cite the Dryad data package:

Sun M, Soltis DE, Soltis PS, Zhu X, Burleigh JG, Chen Z (2014) Data from: Deep phylogenetic incongruence in the angiosperm clade Rosidae. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.7sg58
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