Abstract
SUMMARY: We present Mirage 2.0, which accurately estimates gene-content evolutionary history by considering heterogeneous evolutionary patterns among gene families. Notably, we introduce a deterministic pattern mixture model, which makes Mirage substantially faster and more memory-efficient to be applicable to large datasets with thousands of genomes. AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/fukunagatsu/Mirage. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.