DOI: 10.57760/sciencedb.03104
title: Supplemental data for Modelling compositional heterogeneity resolves deep phylogeny of flowering plants
title: Supplemental data for Modelling compositional heterogeneity resolves deep phylogeny of flowering plants

description: This Readme file summarizes the supplementary tables (Tabs. S1 and S2) and resultant files of our phylogenomic analyses deposited in the ScienceDB repository of the paper:Modelling compositional heterogeneity resolves deep phylogeny of flowering plantsTab. S1. Properties of supermatrices used in the phylogenomic analyses.Tab. S2. Abbreviations for the taxon names used in the phylogenomics analyses.The results of our phylogenomic analyses are listed in three root folders, corresponding to the three previously published studies: Li et al. (2019) Nat. Plants, Xue et al. (2021) J. Syst. Evol. and Yang et al. (2020) Plant Commun. 1-Li et al. 2019: this folder includes two folders, showing results of Bayesian analyses of subsampled plastome matrices of Li et al. (2019). Li-Matrix 1-PhyloBayes-CAT-GTR: 108-taxa matrix under the CAT-GTR model in PhyloBayes.Li-Matrix 2-PhyloBayes-CAT-GTR: 126-taxa matrix under the CAT-GTR model in PhyloBayes. 2-Xue et al. 2021: this folder includes two folders, showing results of Bayesian analyses of mitogenomic nucleotide and amino acid datasets of Xue et al. (2021), respectively.Xue-Matrix 1-PhyloBayes-CAT-GTR-nt: 113-taxa nucleotide (nt) matrix under the CAT-GTR model in PhyloBayes.Xue-Matrix 1-PhyloBayes-CAT-GTR-aa: 113-taxa amino acid (aa) matrix under the CAT-GTR model in PhyloBayes.3-Yang et al. 2020: this folder includes three folders, showing results of both Bayesian and Maximum Likelihood analyses of transcriptome (amino acid) datasets of Yang et al. (2020).1-1594 genes: it includes phylogenomic results based on Matrix 1 under various evolutionary models. Models used in the analyses are incorprated in the file names.  Matrix 1-IQTree-LG+C20-PMSF-53 taxa-BMGE[BLOSUM95-h0.4]Matrix 1-IQTree-LG+C40-PMSF-53 taxa-BMGE[BLOSUM95-h0.4]Matrix 1-IQTree-LG+C60-PMSF-53 taxa-BMGE[BLOSUM95-h0.4]Matrix 1-IQTree-LG4X+R-53 taxa-BMGE[BLOSUM95-h0.4]Matrix 1-PhyloBayes-CAT-GTR-53 taxa-BMGE[BLOSUM95-h0.4]2-756 genes: it includes phylogenomic results based on variants of Matrix 2 (Matrix 2-1, Matrix 2-1-recoded, Matrix 2-2 and Matrix 2-3) under various evolutionary models, and model test based on Matrix 2-3. Models used in the analyses are incorprated in the file names.  Matrix 2-1-IQTree-LG4X+R-57 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-1-PhyloBayes-CAT-GTR-56 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-1-recoded-PhyloBayes-CAT-GTR-56 taxa-BMGE[BLOSUM95-h0.4]-Dayhoff6 RecodedMatrix 2-2-IQTree-LG-C20-29 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-2-IQTree-LG-C40-PMSF-29 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-2-IQTree-LG-C60-PMSF-29 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-2-PhyloBayes-CAT-GTR-29 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-3-model test and tree inferences3-296 genes: : it includes phylogenomic results based on Matrix 3 and Matrix 3-original under various evolutionary models. Models used in the analyses are incorprated in the file names.   Matrix 3-IQTree-LG+C20-PMSF-aa-BMGE[BLOSUM95-h0.4]Matrix 3-IQTree-LG+C60-PMSF-aa-BMGE[BLOSUM95-h0.4]Matrix 3-IQTree-LG4X+R-aa-BMGE[BLOSUM95-h0.4]Matrix 3-Phylobayes-CAT+GTR-aa-BMGE[BLOSUM95-h0.4]Matrix 3-original-Phylobayes-CAT+GTR-aa
description: This Readme file summarizes the supplementary tables (Tabs. S1 and S2) and resultant files of our phylogenomic analyses deposited in the ScienceDB repository of the paper:Modelling compositional heterogeneity resolves deep phylogeny of flowering plantsTab. S1. Properties of supermatrices used in the phylogenomic analyses.Tab. S2. Abbreviations for the taxon names used in the phylogenomics analyses.The results of our phylogenomic analyses are listed in three root folders, corresponding to the three previously published studies: Li et al. (2019) Nat. Plants, Xue et al. (2021) J. Syst. Evol. and Yang et al. (2020) Plant Commun. 1-Li et al. 2019: this folder includes two folders, showing results of Bayesian analyses of subsampled plastome matrices of Li et al. (2019). Li-Matrix 1-PhyloBayes-CAT-GTR: 108-taxa matrix under the CAT-GTR model in PhyloBayes.Li-Matrix 2-PhyloBayes-CAT-GTR: 126-taxa matrix under the CAT-GTR model in PhyloBayes. 2-Xue et al. 2021: this folder includes two folders, showing results of Bayesian analyses of mitogenomic nucleotide and amino acid datasets of Xue et al. (2021), respectively.Xue-Matrix 1-PhyloBayes-CAT-GTR-nt: 113-taxa nucleotide (nt) matrix under the CAT-GTR model in PhyloBayes.Xue-Matrix 1-PhyloBayes-CAT-GTR-aa: 113-taxa amino acid (aa) matrix under the CAT-GTR model in PhyloBayes.3-Yang et al. 2020: this folder includes three folders, showing results of both Bayesian and Maximum Likelihood analyses of transcriptome (amino acid) datasets of Yang et al. (2020).1-1594 genes: it includes phylogenomic results based on Matrix 1 under various evolutionary models. Models used in the analyses are incorprated in the file names.  Matrix 1-IQTree-LG+C20-PMSF-53 taxa-BMGE[BLOSUM95-h0.4]Matrix 1-IQTree-LG+C40-PMSF-53 taxa-BMGE[BLOSUM95-h0.4]Matrix 1-IQTree-LG+C60-PMSF-53 taxa-BMGE[BLOSUM95-h0.4]Matrix 1-IQTree-LG4X+R-53 taxa-BMGE[BLOSUM95-h0.4]Matrix 1-PhyloBayes-CAT-GTR-53 taxa-BMGE[BLOSUM95-h0.4]2-756 genes: it includes phylogenomic results based on variants of Matrix 2 (Matrix 2-1, Matrix 2-1-recoded, Matrix 2-2 and Matrix 2-3) under various evolutionary models, and model test based on Matrix 2-3. Models used in the analyses are incorprated in the file names.  Matrix 2-1-IQTree-LG4X+R-57 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-1-PhyloBayes-CAT-GTR-56 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-1-recoded-PhyloBayes-CAT-GTR-56 taxa-BMGE[BLOSUM95-h0.4]-Dayhoff6 RecodedMatrix 2-2-IQTree-LG-C20-29 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-2-IQTree-LG-C40-PMSF-29 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-2-IQTree-LG-C60-PMSF-29 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-2-PhyloBayes-CAT-GTR-29 taxa-BMGE[BLOSUM95-h0.4]Matrix 2-3-model test and tree inferences3-296 genes: : it includes phylogenomic results based on Matrix 3 and Matrix 3-original under various evolutionary models. Models used in the analyses are incorprated in the file names.   Matrix 3-IQTree-LG+C20-PMSF-aa-BMGE[BLOSUM95-h0.4]Matrix 3-IQTree-LG+C60-PMSF-aa-BMGE[BLOSUM95-h0.4]Matrix 3-IQTree-LG4X+R-aa-BMGE[BLOSUM95-h0.4]Matrix 3-Phylobayes-CAT+GTR-aa-BMGE[BLOSUM95-h0.4]Matrix 3-original-Phylobayes-CAT+GTR-aa