Data from "A comparison of methods for quantifying treelikeness"

Data from "A comparison of methods for quantifying treelikeness"Figshare repository Caitlin Cherryh, 2024OverviewThis Figshare repository contains results from the manuscript "A comparison of methods for quantifying treelikeness". The GitHub repository for this project (https://github.com/caitlinch/treelikeness-metrics/) contains instructions and all scripts necessary to repeat these analyses.Empirical dataWe applied treelikeness metrics to two empirical datasets:<b>Original dataset: </b>Metazoa_Choano_RCFV_strict.phyWhelan N.V., Kocot K.M., Moroz T.P., Mukherjee K., Williams P., Paulay G., Moroz L.L., Halanych K.M., 2017. "Ctenophore relationships and their placement as the sister group to all other animals". Nature Ecology &amp; Evolution. 1:1737–1746 https://doi.org/10.1038/s41559-017-0331-3Whelan N.V., Kocot K.M., Moroz T.P., Mukherjee K., Williams P., Paulay G., Moroz L.L., Halanych K.M., 2017. "Ctenophora Phylogeny Datasets and Core Orthologs". Dataset. Version 1. https://doi.org/10.6084/m9.figshare.4484138.v1 <b>Filtered dataset:</b> 5_Whelan2017MCRS.tar.gzMcCarthy, Charley G, P., Mulhair, P. O., Siu-Ting, K., Creevey, C. J., O’Connell, M. J., 2023. "Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny", Molecular Biology and Evolution, 40:msac276, https://doi.org/10.1093/molbev/msac276McCarthy C. 2022. "ATOLRootStudy", GitHub repository, https://github.com/chmccarthy/ATOLRootStudy (Accessed 18/06/2024)Repository contentsrandomTree_simulation_parameters.csvInput parameters used to generate the simulated alignments for the random tree simulations.randomTree_simulation_treelikeness_metrics_collated_results.csvResults from applying each treelikeness test statistic to each alignment simulated under the random tree simulation scheme.introgression_simulation_parameters.csvInput parameters used to generate the simulated alignments for the introgression simulations.introgression_simulations_treelikeness_metrics_collated_results.csvResults from applying each treelikeness test statistic to each alignment simulated under the introgression simulation scheme.Whelan2017_genes.zipThis directory contains genes extracted from the original Whelan et al. 2017 alignment, separated into partitions using the partition file from the Whelan et al. (2017) studyMcCarthy2023_genes.zipMcCarthy et al. (2023) filtered the above alignment of Whelan et al. (2017) to remove partitions with insufficient evidence of orthology.This directory contains genes extracted from the filtered alignment of McCarthy et al. 2023, separated into partitions using the partition file from the McCarthy et al. (2023) studycollated_gene_output.zipIntermediate results from applying the parametric bootstrap to empirical datasets.A parametric bootstrap was applied to each gene in the Whelan et al. (2017) and McCarthy et al. (2023) alignments to determine whether the null hypothesis of treelikeness could be rejected. To perform the parametric bootstrap, for each gene we generated 99 simulated genes with the same underlying tree and pattern of evolution, then calculated treelikeness metrics for the original gene and all 99 replicates. This directory contains a .csv file for each gene, with a single row containing the treelikeness metric results for the gene and 99 rows containing the treelikeness metric results for each simulated alignment.gene_treelikeness_pvalues.csvFinal parametric bootstrap results (including p-value to assess the null hypothesis of treelikeness) and treelikeness metric results for each gene in both empirical datasets.