AvP detect

Run AvP detect

if fastml was set to false then substitute fasttree for iqtree

avp detect -i [output_dir]/mafftgroups/ -o [output_dir] -g [output_dir]/groups.tsv -t [output_dir]/tmp/taxonomy_nexus.txt -c config.yaml

• The following folders will be created inside output dir
  • fasttree phylogenetic results in newick format for each group
  • fasttree_nexus phylogenetic results in nexus format for each group. These are best for visualisation with the a tree viewer program like FigTree
• The following files will be created inside output dir
  • fasttree_general_results.txt shows general results for the analyses
  • fasttree_tree_results.txt shows the result for each protein

Output files

• fasttree_tree_results.txt

  • It is a tsv file with no header with the following format

    result	alignment_file	tree_file	protein_name

  • The result can be one of the following

    • HGT-NT: There weren't any TOI proteins and thus the protein is a de facto HGT
    • HGT: The phylogenetic tree supports the HGT hypothesis
    • NO-OT: Only TOI proteins were present
    • NO: The phylogenetic tree doesn't support the HGT hypothesis
    • COMPLEX: The topology of the phylogenetic tree couldn't give definitive results