A comparison of phylogenomic inference pipelines for low-coverage whole-genome sequencing in Formica ants

Using 36 low coverage whole genome sequences from the ant genus Formica, we compared different analytical pipelines to determine the strengths and weaknesses of common approaches to conduct phylogenetic research on resequenced genomes. Most of the Formica ant genomes used in this project were produced for a previous project, but we added a male that is a hybrid between Formica pacifica and Formica transmontanis.