Data from: Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies

Richart C, Hayashi C, Marshal H

Date Published: December 21, 2015

DOI: http://dx.doi.org/10.5061/dryad.3mr26

 

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Title all5_672loci_nex
Downloaded 19 times
Description Nexus alignments of 672 loci containing transcriptomic sequence data from Trogulus, Ortholasma, Hesperonemastoma, Acuclavella, and Sabacon.
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Title 672lociCharacterizations_all5Dyspnoi
Downloaded 27 times
Description An .xls file characterizing aspects of the 672 loci used in phylogenetic analyses, including: evolutionary rates and branch lengths, AT and AT3 content, bootstrap distributions, subsampled loci, hidden support analyses, and concordance factors.
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Title all5_672loci_concatRAxML
Downloaded 18 times
Description Alignment and partitions file for the concatenated RAxML analysis of 672 loci
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Title all5_672loci_PhyML-trees
Downloaded 21 times
Description 672 gene trees generated via PhyML
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Title all5_672loci_PhyML-BootstrapTrees
Downloaded 13 times
Description 100 bootstrap trees for each of 672 loci analyses in Newick format
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Title all5_672loci_MrBayes_treFiles
Downloaded 19 times
Description A MrBayes consensus tree and the tree files from each (2) runs for 672 loci
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Title RandomGeneSets
Downloaded 12 times
Description The loci used for subsampled data. This includes 80 total subsampes, 10 each for 25, 50, 100, 200, 300, 400, 500, and 600 subsampled loci. This includes partition files for concatenated analyses, and the resulting tree files for MP-EST, STAR, and concatenated RAxML analyses.
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Title ep_NexusAlignments
Downloaded 16 times
Description Alignments for 14 loci and these loci concatenated for expanded panel analyses in Nexus format.
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Title ep_RAxML_GeneTrees
Downloaded 15 times
Description RAxML gene trees for 14 loci used in expanded panel analyses.
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Title ep_ModelsEvolution
Downloaded 13 times
Description Results from models of evolution analyses used in expanded panel analyses, returned from jModelTest and PartitionFinder.
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When using this data, please cite the original publication:

Richart C, Hayashi C, Marshal H (2015) Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Molecular Phylogenetics and Evolution 95: 171–182. http://dx.doi.org/10.1016/j.ympev.2015.11.010

Additionally, please cite the Dryad data package:

Richart C, Hayashi C, Marshal H (2015) Data from: Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3mr26
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