Data from: Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

Borowiec ML, Lee EK, Chiu JC, Plachetzki DC

Date Published: November 28, 2015

DOI: http://dx.doi.org/10.5061/dryad.k6tq2

 

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Title Binned Analyses
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Description Results of ML analyses of matrices binned according to rate of locus evolution. Separate analyses were carried out for 60-, 108-, and 216-locus bins. The text files contain support for the topologies of interest.
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Title Code
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Description Scripts used in analyses and plotting selected figures. See also https://github.com/marekborowiec/metazoan_phylogenomics/blob/master/gene_stats.R
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Title Partition Statistics
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Description Spreadsheet containing data for all of the partition-specific statistics used to construct the various matrices described in the paper.
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Title Jackknife
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Description Results of 108-locus and 20-locus jackknife analyses. See Figure 3.
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Title Data Matrices
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Description All concatenated matrices in PHYLIP and NEXUS formats. The names of the concatenated matrices correspond to Table 1.
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Title Orthologous Groups
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Description Trimmed alignments for each of 1,161 orthologous groups recovered from OrhtologID analyses of gene models from the 36 metazoan and outgroup genomes.
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Title OrthologID Output
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Description Data partitions from OrthologID aligned and in NEXUS format. "full" dataset includes all orthologs recovered and "m27" includes only partitions present in at least 27 taxa.
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Title PartitionFinder Results
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Description Control files, data and results for all PartitionFinder analyses on concatenated matrices conducted in the study.
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Title PhyloBayes Results
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Description Results of all PhyloBayes analyses conducted in the study including Bayesien posterior densities and traces of selected parameters as well as consensus trees.
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Title Progressive Concatenation Data and Results
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Description Matrices and RAxML result files from progressive concatenation analyses presented in order of slow- to fast-evolving loci.
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Title RAxML Concatenated
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Description Data matrices and results from all RAxML analyses of concatenated datasets described in the study
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Title RAxML_single_genes
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Description Results for each of 1,080 single gene RAxML analyses
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Title Single Gene Alignments
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Description Trimmed alignments for all 1080 loci in FASTA format.
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Title Taxonomic Descriptions
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Description This spreadsheet contains taxonomic information on the species used in the present study.
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Title Topology_tests
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Description Results of Bayesian tests of topology carried out in MrBayes. Subfolder names correspond to alternative topologies tested. See Table 2 and manuscript text for explanations.
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When using this data, please cite the original publication:

Borowiec ML, Lee EK, Chiu JC, Plachetzki DC (2015) Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics 16: 987. http://dx.doi.org/10.1186/s12864-015-2146-4

Additionally, please cite the Dryad data package:

Borowiec ML, Lee EK, Chiu JC, Plachetzki DC (2015) Data from: Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.k6tq2
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