Phyloformer: Fast, accurate and versatile phylogenetic reconstruction with deep neural networks

This record is composed of: The results.tar.gz file which contains all the output files necessary to reproduce the figures and tables from the linked paper The 3 datasets used to fine tune different versions of Phylofofmer: cherry_fine_tune.tar.xz used to fine tune Phyloformer on the CherryML model LG_fine_tune_mre.tar.xz used to fine tune Phyloformer on LG+GC data with an MRE loss pastek_fine_tune.tar.xz used to fine tune Phyloformer on the SelReg model The paper_test_sets.tar.xz file contains the test sets used to generate data in results.tar.gz, with simulated tree/msa pairs and trees inferred by different methods