README.md

Maximum likelihood phylogenetic trees

This analysis uses:

• MAFFT v7.525: https://mafft.cbrc.jp/alignment/software/
• IQTree v2.1.4: http://www.iqtree.org/
• TreeTime v0.11.3: https://treetime.readthedocs.io/

File structure

• ML_Trees
  • segments (HA, NA, etc.)
    • FASTA file
    • Alignment file
    • ML Tree file
    • treetime_host_mugration
      • Tree file with host annotations
      • Confidence file
      • GTR file
  • TreePDFs
    • PDF tree files for each segment

Step-by-step:

1. Align FASTA file (mafft --thread -1 fasta_file > alignment_file)
2. Using deflines from alignment files, make a metadata csv file
3. Build ML phylogenetic tree (iqtree -T AUTO -s alignment_file -m MFP -B 1000 --bnni --alrt 1000)
4. Run TreeTime mugration inference (treetime mugration --tree treefile --states meta.csv --attribute host-category --confidence)