AvP classify

Run AvP classify

1. Create classification.txt file (a sample file for non Metazoan to Metazoan HGTS can be found under AvP/depot/)

• See classification.txt

[!] If the analysis does not use Metazoa as ingroup you have to change the classification file to include the Metazoa rank as shown below

#rank members
Eukaryota	Eukaryota;Viridiplantae;Fungi;Oomycota;Metazoa
Prokaryota	Bacteria;Archaea
Viriods	Viroids
Viruses	Viruses

2. Run the avp classify command

avp classify -i [output_dir]/fasttree_nexus/ -t [output_dir]/fasttree_tree_results.txt -f [classification.txt] -c config.yaml -o [output_dir] (-a [ai.out])

• [Optional] If the ai.out is provided the Ingroup classification will contain the excluded queries as well.
• The following folders will be created inside output dir
  • classification Inside the folder are folders based on the classification file. Each folder contains the nexus for each gene classfied as such.
• The following file will be created inside output dir
  • classification_results.txt shows general results for the analyses
  • classification_tree_results.txt shows the result for each protein