DOI: 10.57760/sciencedb.03302
title: Supplemental Data for Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings
title: Supplemental Data for Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewings

description: This Readme file summarizes the resultant files of our phylogenomic analyses deposited in the Science Data Bank repository of the paper:Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewingsThe results of our phylogenomic analyses are given in two root folders, corresponding to the three previously published studies: Vasilikopoulos et al. (2020) and Winterton et al. (2018).1-reanalyses of Vasilikopoulos et al. 2020: this folder includes two folders, showing results of phylogenomic analyses of subsampled transcriptomic matrices of Vasilikopoulos et al. (2020). iqtree-LG4X+R-Matrix A-BMGE_BLOSUM62 -h0.1-0.4: 49-taxa matrix (trimmed using BMGE, setting: BLOSUM62 -h 0.1:0.4) under the LG4X+R model in IQ-Tree.phylobayes-CAT-GTR-Matrix A-BMGE_BLOSUM62 -h0.1-0.4: 49-taxa matrix (trimmed using BMGE, setting: BLOSUM62 -h 0.1:0.4) under the CAT-GTR model in PhyloBayes.2-reanalyses of Winterton et al. 2018: this folder includes three folders, showing results of both Bayesian and Maximum Likelihood analyses of AHE (nucleotide and amino acid) datasets of Winterton et al. (2018) and model testing.  NT: this folder includes two folders, showing results of Bayesian analyses of AHE nucleotide (NT) datasets of Winterton et al. (2018).  1-phylobayes-cat-gtr-137-taxa-nt: 137-taxa matrix under the CAT-GTR model in PhyloBayes.2-phylobayes-cat-gtr-133-taxa-nt-rogue taxa removed: 133-taxa matrix under the CAT-GTR model in PhyloBayes. AA: this folder includes three folders, showing results of Bayesian analyses of AHE amino acid (AA) dataset of Winterton et al. (2018).  3-iqtree-LG4X+R-137taxa: 137-taxa matrix under the LG4X+R model in IQ-Tree.4-iqtree-LG+C60-137taxa: 137-taxa matrix under the LG+C60 model in IQ-Tree.5-phylobayes-CAT-GTR-137taxa-focal tree: 137-taxa AA matrix under the CAT-GTR model in PhyloBayes; it is our focal tree, shown as Fig.1 of the paper.Model Test [based on AA dataset]: model testing of the AHE amino acid dataset of Winterton et al. (2018) using PhyloBayes.  
description: This Readme file summarizes the resultant files of our phylogenomic analyses deposited in the Science Data Bank repository of the paper:Improved modelling of compositional heterogeneity reconciles phylogenomic conflicts among lacewingsThe results of our phylogenomic analyses are given in two root folders, corresponding to the three previously published studies: Vasilikopoulos et al. (2020) and Winterton et al. (2018).1-reanalyses of Vasilikopoulos et al. 2020: this folder includes two folders, showing results of phylogenomic analyses of subsampled transcriptomic matrices of Vasilikopoulos et al. (2020). iqtree-LG4X+R-Matrix A-BMGE_BLOSUM62 -h0.1-0.4: 49-taxa matrix (trimmed using BMGE, setting: BLOSUM62 -h 0.1:0.4) under the LG4X+R model in IQ-Tree.phylobayes-CAT-GTR-Matrix A-BMGE_BLOSUM62 -h0.1-0.4: 49-taxa matrix (trimmed using BMGE, setting: BLOSUM62 -h 0.1:0.4) under the CAT-GTR model in PhyloBayes.2-reanalyses of Winterton et al. 2018: this folder includes three folders, showing results of both Bayesian and Maximum Likelihood analyses of AHE (nucleotide and amino acid) datasets of Winterton et al. (2018) and model testing.  NT: this folder includes two folders, showing results of Bayesian analyses of AHE nucleotide (NT) datasets of Winterton et al. (2018).  1-phylobayes-cat-gtr-137-taxa-nt: 137-taxa matrix under the CAT-GTR model in PhyloBayes.2-phylobayes-cat-gtr-133-taxa-nt-rogue taxa removed: 133-taxa matrix under the CAT-GTR model in PhyloBayes. AA: this folder includes three folders, showing results of Bayesian analyses of AHE amino acid (AA) dataset of Winterton et al. (2018).  3-iqtree-LG4X+R-137taxa: 137-taxa matrix under the LG4X+R model in IQ-Tree.4-iqtree-LG+C60-137taxa: 137-taxa matrix under the LG+C60 model in IQ-Tree.5-phylobayes-CAT-GTR-137taxa-focal tree: 137-taxa AA matrix under the CAT-GTR model in PhyloBayes; it is our focal tree, shown as Fig.1 of the paper.Model Test [based on AA dataset]: model testing of the AHE amino acid dataset of Winterton et al. (2018) using PhyloBayes.