fCAT process

fCAT algorithm consists of 3 main steps:

1. Calculate group-specific cutoffs for a core set

Please make sure that the R dependency are available before running this function.

fcat.cutoff --coreDir /path/to/fcat_data --coreSet eukaryota

2. Search for orthologs in a gene set of interst and create phylogenetic profiles

fcat.ortho --coreDir /path/to/fcat_data --coreSet eukaryota --refspecList "HOMSA@9606@2" --querySpecies /path/to/query.fa --annoQuery /path/to/query.json

3. Create report for completeness assessment

fcat.report --coreDir /path/to/fcat_data --coreSet eukaryota --outDir /path/to/fcat/output --queryID queryID --mode 1