Data from: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

Longo SJ, Faircloth BC, Meyer A, Westneat MW, Alfaro ME, Wainwright PC

Date Published: May 9, 2017

DOI: http://dx.doi.org/10.5061/dryad.v7f76

 

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 NCBI Accession Information
Downloaded 7 times
Description Text file indicating accession numbers for raw-reads in NCBI SRA and accession numbers for assembled UCE contigs for each species in NCBI GenBank.
Download AccessionInfo.txt (8.022 Kb)
Details View File Details
Title UCE alignments
Downloaded 5 times
Description Cleaned and trimmed MAFFT alignments for each UCE in the 75 and 95 percent complete matrices
Download uce_alignments.zip (5.867 Mb)
Details View File Details
Title Concatenated alignments of UCEs
Downloaded 5 times
Description Concatenated alignments and charsets for the 95p and 75p matrices used in ExaBayes and RAxML analyses, as well as best-fit partitioning schemes from Partition Finder and RY-coded matrices.
Download concatenated_alignments.zip (21.44 Mb)
Details View File Details
Title ASTRAL files
Downloaded 11 times
Description Input and output files for all ASTRAL analyses of 75p and 95p matrices
Download ASTRAL_input_output.zip (174.5 Mb)
Details View File Details
Title Phylogenetic Trees
Downloaded 8 times
Description Files containing all trees presented in the publication
Download trees.zip (31.19 Kb)
Details View File Details
Title Trinity Assemblies
Downloaded 6 times
Description De novo Trinity assemblies of raw-reads for all individuals included in our published study.
Download trinity_assemblies_dryad.zip (304.6 Mb)
Details View File Details
Title ExaBayes output
Downloaded 6 times
Description Input and output files for the ExaBayes analyses of the 75p and 95p datasets
Download ExaBayes_output.zip (114.0 Mb)
Details View File Details

When using this data, please cite the original publication:

Longo SJ, Faircloth BC, Meyer A, Westneat MW, Alfaro ME, Wainwright PC (2017) Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements. Molecular Phylogenetics and Evolution 113: 33-48. http://dx.doi.org/10.1016/j.ympev.2017.05.002

Additionally, please cite the Dryad data package:

Longo SJ, Faircloth BC, Meyer A, Westneat MW, Alfaro ME, Wainwright PC (2017) Data from: Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.v7f76
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: