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 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

  Result	Description
  HGT-NT	There weren't any Ingroup proteins and thus the protein is a de facto HGT
  HGT	The phylogenetic tree supports the HGT hypothesis
  NO-OT	Only Ingroup 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
  UNKNOWN	The proteins in the tree are of unknown origin