Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps

Data Description<br>Simulated_Data: This directory contains a simulated DNA sequence alignment (Simulated_data.fasta) with 446 sequences and 134131 sites. This dataset was simulated under auto correlated evolutionary rates among lineages. A set of 100 genes were simulated using a wide range of realistic biological parameters. The Simulated_data is the concatenation of these simulated genes. The tree file (Sim_candiate_tree.nwk) is the candidate tree for this dataset. Fig 2(a) –(d) in the main text have been produced by analyzing this dataset. Small_datasets: This directory contains three single-gene DNA sequence datasets with 446 species and 4000 to 10000 sites. The tree file (Small_data_candidate_tree.nwk) is used as a candidate tree for the analysis. Fig 2(e)-(f) have been produced by analyzing these datasets. Empirical_Mammal_Dataset: The empirical DNA sequence dataset has been provided in this directory. The eutherian mammal dataset consists of 447 nuclear genes and 37 mammalian species sequences. The concatenated sequence alignment has 1,391,742 sites. The tree file (MAM2_candiate_tree.nwk) is the candidate tree for this empirical dataset. Large_Simulated_Datasets: There are five different simulated DNA sequence datasets, all with 446 species and a varying number of sites (pnas_test_50k: 50,000 sites, pnas_test_100k: 100,000 sites, pnas_test_200k: 200,000 sites, pnas_test_400k: 400,000 sites, pnas_test_all: 536,534 sites). The first four datasets were generated by a random sample of sites from the pnas_test_all dataset. The pnas_test_all.fasta sequence alignment was generated by concatenating four sets of randomly selected 100 genes which were simulated using different rate variation models. Fig 2(g) has been produced by analyzing these datasets. <br>