Data from: Scoutknife: A naïve, whole genome informed phylogenetic robusticity metric

The phylogenetic bootstrap, first proposed by Felsenstein in 1985, is a critically important statistical method in assessing the robusticity of phylogenetic datasets. Core to its concept was the use of pseudosampling - assessing the data by generating new replicates derived from the initial dataset that was used to generate the phylogeny. In this way, phylogenetic support metrics could overcome the lack of perfect, infinite data. With infinite data, however, it is possible to sample smaller replicates directly from the data to obtain both the phylogeny and its statistical robusticity in the same analysis. Due to the growth of whole genome sequencing, the depth and breadth of our datasets have greatly expanded and are set to only expand further. With genome-scale datasets comprising thousands of genes, we can now obtain a proxy for infinite data. Accordingly, we can potentially abandon the notion of pseudosampling and instead randomly sample small subsets of genes from the thousands of genes in our analyses. Here, we introduce Scoutknife, a jackknife-style subsampling implementation that generates 100 datasets by randomly sampling a small number of genes from an initial large-gene dataset to jointly establish both a phylogenetic hypothesis and assess its robusticity. Using 18 previously published datasets and 100 simulation studies, we show that Scoutknife is conservative and informative as to conflicts and incongruence across the whole genome, without the need for subsampling based on traditional model selection criteria.