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 g..., Dataset Construction and Analysis
            For both real and simulation analyses (for details see below), 100 genes were randomly selected 100 times from the source datasets, generating 100 100-gene concatenated sample datasets using the Scoutknife Package (https://github.com/JFFleming/Scoutknife). The Scoutknife script package requires catsequences23 to be installed as a prerequisite, available at (https://github.com/ChrisCreevey/catsequences).
            Phylogenies for each Scoutknife dataset were constructed under IQ-Tree v1.6.1224 using Modeltest25, with a separate model applied to each gene and no partition merging. As a data density-based technique, Scoutknife might be expected to perform better in high data density scenarios where partitions can be comfortably merged. As such, this was intended to limit the efficacy of Scoutknife further and test its performance under a scenario with more highly variable best fit models than might be expected under normal conditions, whilst ..., Data Files can all be opened in any text editor.
Supplementary files in the Tables category are in Excel format, and can be opened by LibreOffice
Scoutknife is available at https://github.com/JFFleming/Scoutknife