**OutputFolderName**
The folder where the output files are stored.
Blast
Folder containing BLASTp database, BLASTp output files, master file, self-score folder, and translation files.
Blast_db_prot
Folder containing the BLASTp database.
Blast_db_protein.pdb
Position-specific Data Base file. Contains position-specific scoring matrices (PSSMs) used in PSI-BLAST searches.
Blast_db_protein.phr
Protein Header Record file. Contains the header information for each sequence in the protein database.
Blast_db_protein.pin
Protein Index file. Contains the index of the sequences in the protein database.
Blast_db_protein.pog
Protein Organism Group file. Contains information about the taxonomic grouping of the sequences in the protein database.
Blast_db_protein.pos
Protein Organism Sequence file. Contains the actual sequence data for the protein database.
Blast_db_protein.pot
Protein Organism Taxonomy file. Contains taxonomic information for the sequences in the protein database.
Blast_db_protein.psq
Protein Sequence Query file. Contains the sequence data in a format optimized for BLAST searches.
Blast_db_protein.ptf
Protein Taxonomy File. Contains taxonomy information for the sequences in the protein database.
Blast_db_protein.pto
Protein Taxonomy Organism file. Contains organism-specific taxonomy information for the sequences in the protein database.
Blast_output
Folder containing the BLASTp output files.
blast_results_x.tsv
TSV file containing the BLASTp results for the locus x.
blast_results_y.tsv
TSV file containing the BLASTp results for the locus y.
blast_results_z.tsv
TSV file containing the BLASTp results for the locus z.
...
All the other TSV BLASTp results files.
master_file.fasta
FASTA file containing all the protein sequences used in the analysis (used to create BLAST DB).
self_score_folder
Folder containing the self-score BLAST results.
blast_results_x.tsv
TSV file containing the BLASTp results for self-score for the locus x.
blast_results_y.tsv
TSV file containing the BLASTp results for self-score for the locus y.
blast_results_z.tsv
TSV file containing the BLASTp results for self-score for the locus z.
...
All the other TSV BLASTp for self-score results files.
Translation
Folder containing the translation files.
x_translation.fasta
FASTA file containing the translation for the locus x.
y_translation.fasta
FASTA file containing the translation for the locus y.
z_translation.fasta
FASTA file containing the translation for the locus z.
...
All the other translation files.
**paralogous_annotations.tsv**
TSV file with the clusters that should be joined as well as the annotations for each locus.
Only with the -ann option.
**paralogous_loci_final_recommendations.tsv**
TSV with the loci clusters (one locus per row) with the action to be taken (always 'Join'). The clusters are separated by a row with a '#'.
The clusters here differ from the ones in paralogous_loci_report_cluster_by_id.tsv because it consists of only the loci that passed certain checks.
**paralogous_loci_report.tsv**
TSV file containing the report of the paralogous loci. Here we can see which loci pass the checks to be considered paralogs that can be joined.
**paralogous_loci_report_cluster_by_id.tsv**
TSV file containing the report of the paralogous loci clustered by ID.
Only with the --nocleanup option.