Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title 129 taxa
Downloaded 47 times
Description Zip file of full datasets. Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file. Note, no taxa are excluded, although in final analyses rogue taxa are removed.
Download 129tax.zip (1.325Mb)
Details View File Details
Title 16 taxa
Downloaded 42 times
Description Zip file of reduced taxon datasets (16 exemplar taxa). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.
Download 16tax.zip (401.8Kb)
Details View File Details
Title Individual Genes
Downloaded 43 times
Description 75 individual gene datasets. All datasets start with the first codon position.
Download IndividualGenes.zip (296.6Kb)
Details View File Details
Title 31 genes
Downloaded 32 times
Description Zip file of reduced gene datasets (corresponding to turtle question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file. Note, taxon sampling has been reduced by removing rogue taxa.
Download 31genes.zip (413.6Kb)
Details View File Details
Title 26 genes
Downloaded 40 times
Description Zip file of reduced gene datasets (corresponding to Lissamphibia question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file. Note, taxon sampling has been reduced by removing rogue taxa.
Download 26genes.zip (297.7Kb)
Details View File Details
Title 16taxa 31genes
Downloaded 37 times
Description Zip file of reduced gene and 16 taxa datasets (corresponding to turtle question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.
Download 16tax-31genes.zip (139.9Kb)
Details View File Details
Title 16taxa 26genes
Downloaded 39 times
Description Zip file of reduced gene and 16 taxa datasets (corresponding to Lissamphibia question). Included are 8 files corresponding to 4 datasets 1)NUCL (nucleotide) based dataset and partition file (partitioned by codon n12 and n3), 2) N12 (excluding 3rd codon) dataset and partition file (by gene), 3) AA (amino acid) dataset and partition file (by gene), 4) DEGEN1 (nucleotide-based accounting for codon degeneracy) based dataset with partition file.
Download 16tax-26genes.zip (101.2Kb)
Details View File Details
Title Simulated Data
Downloaded 35 times
Description Two simulated datasets used in study
Download SimulatedData.zip (4.43Kb)
Details View File Details
Title Slow Genes
Downloaded 45 times
Description Data and partition file for the reduced gene dataset, removing the 19 most quickly evolving genes. Partition is by gene.
Download SlowGenes.zip (398.7Kb)
Details View File Details

When using this data, please cite the original publication:

Fong JJ, Brown JM, Fujita MK, Boussau B (2012) A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia. PLoS ONE 7(11): e48990. http://dx.doi.org/10.1371/journal.pone.0048990

Additionally, please cite the Dryad data package:

Fong JJ, Brown JM, Fujita MK, Boussau B (2012) Data from: A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic Lissamphibia. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.25j6h
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)