Data from: Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes

Chen X, Lemmon AR, Lemmon EM, Pyron RA, Burbrink FT

Date Published: April 17, 2017

DOI: http://dx.doi.org/10.5061/dryad.r43s0

 

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 gene_fasta_87taxa
Downloaded 10 times
Description Genes used to build the phylogeny
Download gene_fasta_87taxa.zip (1.896 Mb)
Details View File Details
Title Species tree from MPEST
Downloaded 7 times
Description Time-calibrated species tree using MPEST for topological inference and MCMCtree for the time
Download tree_oldcal.tre (6.336 Kb)
Details View File Details
Title Species tree inferred using ASTRAL
Downloaded 5 times
Download rat_astral_II.tre (3.761 Kb)
Details View File Details
Title gene trees for each locus
Downloaded 6 times
Description Gene trees were built using Bayesian inference method with 1000 posterior probability trees saved in each file. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"
Download rootedtrees-20170409T045003Z-001.zip (371.0 Mb)
Details View File Details
Title bootstrap gene trees for each locus
Downloaded 5 times
Description Gene trees were built using maximum likelihood method with 1000 bootstrap gene trees saved in each file. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"
Download bstree_1000-20170409T044850Z-001.zip (426.6 Mb)
Details View File Details
Title maximum likelihood gene tree for each locus
Downloaded 5 times
Description The gene tree for each locus inferred using Maximum likelihood method. These gene trees were used to calculate the among loci gene tree distance only. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"
Download mltrees304.zip (509.4 Kb)
Details View File Details
Title Gene tree for each locus inferred using Bayesian inference method
Downloaded 8 times
Description These gene trees were used to calculate the among loci gene tree distance only. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"
Download ppcontrees.zip (468.8 Kb)
Details View File Details
Title convert full sequence code to full species name
Downloaded 6 times
Description This is a bash script used to convert the tip names on species tree from sequence code to full species names
Download changetreetipnames.sh (5.47 Kb)
Details View File Details
Title convert sequence code to full species name
Downloaded 5 times
Description This is a bash script used to convert the tip names on species tree from full species name to short sequence code.
Download changetreetipnames2.sh (5.47 Kb)
Details View File Details

When using this data, please cite the original publication:

Chen X, Lemmon AR, Lemmon EM, Pyron RA, Burbrink FT (2017) Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes. Molecular Phylogenetics and Evolution 111: 206-218. http://dx.doi.org/10.1016/j.ympev.2017.03.017

Additionally, please cite the Dryad data package:

Chen X, Lemmon AR, Lemmon EM, Pyron RA, Burbrink FT (2017) Data from: Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.r43s0
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: