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.

本数据集来自《量化树状性（treelikeness）的方法比较》一文，托管于Figshare仓库，作者为Caitlin Cherryh，发布于2024年。
概述 本Figshare仓库包含论文《量化树状性（treelikeness）的方法比较》的相关研究结果。本项目的GitHub仓库（https://github.com/caitlinch/treelikeness-metrics/）提供了复现该分析所需的操作指南与全部脚本。
实证数据集 本研究将树状性指标应用于两组实证数据集：
<b>原始数据集：</b>Metazoa_Choano_RCFV_strict.phy
引用来源：Whelan N.V.、Kocot K.M.、Moroz T.P.、Mukherjee K.、Williams P.、Paulay G.、Moroz L.L.、Halanych K.M.，2017年，"Ctenophore relationships and their placement as the sister group to all other animals"，《自然生态与进化》，1卷：1737–1746，https://doi.org/10.1038/s41559-017-0331-3
Whelan N.V.、Kocot K.M.、Moroz T.P.、Mukherjee K.、Williams P.、Paulay G.、Moroz L.L.、Halanych K.M.，2017年，"Ctenophora Phylogeny Datasets and Core Orthologs"，数据集，版本1，https://doi.org/10.6084/m9.figshare.4484138.v1
<b>过滤后数据集：</b>5_Whelan2017MCRS.tar.gz
引用来源：McCarthy, Charley G, P.、Mulhair, P. O.、Siu-Ting, K.、Creevey, C. J.、O’Connell, M. J.，2023年，"Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny"，《分子生物学与进化》，40卷：msac276，https://doi.org/10.1093/molbev/msac276
McCarthy C.，2022年，"ATOLRootStudy"，GitHub仓库，https://github.com/chmccarthy/ATOLRootStudy（访问日期：2024年6月18日）
仓库内容
randomTree_simulation_parameters.csv：用于随机树模拟的比对序列生成的输入参数文件。
randomTree_simulation_treelikeness_metrics_collated_results.csv：针对随机树模拟方案下生成的所有比对序列，应用各树状性检验统计量得到的结果汇总文件。
introgression_simulation_parameters.csv：用于渐渗模拟的比对序列生成的输入参数文件。
introgression_simulations_treelikeness_metrics_collated_results.csv：针对渐渗模拟方案下生成的所有比对序列，应用各树状性检验统计量得到的结果汇总文件。
Whelan2017_genes.zip：该压缩包包含从Whelan等人2017年的比对序列中提取的基因，依据Whelan等人（2017）研究中的分区文件划分为不同分区。
McCarthy2023_genes.zip：McCarthy等人（2023）对Whelan等人（2017）的比对序列进行过滤，移除了同源性证据不足的分区。该压缩包包含从McCarthy等人2023年的过滤后比对序列中提取的基因，依据McCarthy等人（2023）研究中的分区文件划分为不同分区。
collated_gene_output.zip：针对实证数据集应用参数自助法（parametric bootstrap）得到的中间结果文件。本研究对Whelan等人（2017）与McCarthy等人（2023）比对序列中的每个基因应用参数自助法，以检验是否可以拒绝树状性的原假设。具体操作如下：对每个基因，生成99个具有相同系统发育树基础结构与进化模式的模拟基因，随后计算原始基因与全部99个模拟比对序列的树状性指标。该压缩包包含每个基因对应的.csv文件，每个文件包含一行原始基因的树状性指标结果，以及99行对应各模拟比对序列的树状性指标结果。
gene_treelikeness_pvalues.csv：两组实证数据集各基因的最终参数自助法结果（包含用于评估树状性原假设的p值）与树状性指标结果汇总文件。