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:
  1. cherry_fine_tune.tar.xz used to fine tune Phyloformer on the CherryML model
  2. LG_fine_tune_mre.tar.xz used to fine tune Phyloformer on LG+GC data with an MRE loss
  3. 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