Welcome to the auto-phylo manual!

Auto-Phylo

• What is auto-phylo?
• How to run auto-phylo
• auto-phylo script basic structure
• Test data
  • Running times

Built-in modules

• BLAST
  • tblastx
• FASTA file processing
  • add_taxonomy
  • CGF_and_CGA_CDS_processing
  • check_contamination
  • disambiguate
  • merge
  • prefix
  • prefix_out
  • remove_stops
• Alignment
  • Clustal_Omega
  • Clustal_Omega_codons
  • T-coffee
  • T-coffee_codons
• Tree building
  • Fasttree
  • me_tree
  • ml_tree
  • mp_tree
  • MrBayes
  • nj_tree
  • tree_collapser
  • upgma_tree
• Model checking
  • JModel_test
• Special
  • split

References

• Bibliography