Welcome to the Auto-Phylo v2 manual!

Auto-Phylo v2

• What is auto-phylo?
• How to run auto-phylo
• auto-phylo script basic structure
• Test data
  • Modules used
  • Running times
• Pipeliner (GUI)
  • Installation
  • Loading / Creating a pipeline
  • Editing a pipeline
  • Viewing the pipeline
  • Running the pipeline
  • Changing the theme

Built-in modules

• Modules configuration
• BLAST
  • blastn
  • tblastn
  • tblastx
• FASTA file processing
  • add_refs
  • add_taxonomy
  • CGF_and_CGA_CDS_processing
  • check_contamination
  • disambiguate
  • merge
  • prefix
  • prefix_out
  • remove_stops
• Alignment
  • Clustal_Omega
  • Clustal_Omega_codons
  • Mafft
  • Mafft_codons
  • Probcons
  • Probcons_codons
  • Probcons_refinement
  • T-coffee
  • T-coffee_codons
• Tree building
  • get_phylo_taxa
  • Fasttree
  • Fastroot
  • me_tree
  • ml_tree
  • mp_tree
  • MrBayes
  • nj_tree
  • Rootdigger
  • tree_collapse
  • upgma_tree
• Model checking
  • JModel_test
• Gene annotation
  • CGA
• Detection of positively selected amino acid sites
  • ipssa
• Divergence estimates
  • kaks
• Special
  • split

References

• Bibliography