The Phylogenomics activity area of the Genomics for Australian Plants consortium aimed to assemble the Australian Angiosperm Tree of Life (AAToL) and to build bioinformatic tools for phylogenomic projects conducted by Australian taxonomists. In its first stage, Australian native flowering plants were sampled at one specimen per genus by a collaboration of six teams, each centred on a major herbarium. Additional sequences were obtained from data exchange with the Plant and Fungal Tree of Life consortium, who were aiming to reconstruct a phylogeny of global scale with the same sampling approach and homologous sequence markers. After several iterative rounds of analysis, the AAToL ‘big tree’ comprising 2,006 terminals has been inferred, and we are preparing its publication. Stage 2 of the phylogenomics activity produced species-level datasets for selected taxonomic groups. I will present the methodology used in this project, the analysis pipeline that was built for it, and technical problems we encountered along the way that may be of interest to other projects using similarly large phylogenomic datasets.