The Y chromosome is a reliable marker for deep-time phylogenetic inference

Datasets used in Alexader E.P., Foley N.M., and Murphy W.J. In Review. The Y chromosome is a reliable marker for deep-time phylogenetic inference. To access code used in this manuscript, please refer to our GitHub. This repository includes the following: S1 - all of the maximum-likelihood phylogenies generated under concatenation S2 - data related to the gene conversion analysis S3 - input genomes and alignment generated using Progressive Cactus S4 - all filtered and subsetted alignments used to generate trees S5 - accelerated, neutral, and conserved quintile ranges and phyloP score files S6 - trees generated under multi-species coalescence S7 - hypotheses used to perform alternative tree tests S8 - contains the data generated using our novel pipeline, Identi-Y-er, which identifies Y-linked scaffolds in scaffolded genome assemblies