**OutputFolderName**
The folder where the output files are stored.
blast_processing
Folder containing BLASTp database, BLASTp output files, master file, self-score folder, and translation files.
subject_reps_vs_reps_blastdb
Folder containing the BLASTp database for the rep vs rep analysis.
subject_reps_vs_reps_blastdb.pdb
Position-specific Data Base file. Contains position-specific scoring matrices (PSSMs) used in PSI-BLAST searches.
subject_reps_vs_reps_blastdb.phr
Protein Header Record file. Contains the header information for each sequence in the protein database.
subject_reps_vs_reps_blastdb.pin
Protein Index file. Contains the index of the sequences in the protein database.
subject_reps_vs_reps_blastdb.pog
Protein Organism Group file. Contains information about the taxonomic grouping of the sequences in the protein database.
subject_reps_vs_reps_blastdb.pos
Protein Organism Sequence file. Contains the actual sequence data for the protein database.
subject_reps_vs_reps_blastdb.pot
Protein Organism Taxonomy file. Contains taxonomic information for the sequences in the protein database.
subject_reps_vs_reps_blastdb.psq
Protein Sequence Query file. Contains the sequence data in a format optimized for BLAST searches.
subject_reps_vs_reps_blastdb.ptf
Protein Taxonomy File. Contains taxonomy information for the sequences in the protein database.
subject_reps_vs_reps_blastdb.pto
Protein Taxonomy Organism file. Contains organism-specific taxonomy information for the sequences in the protein database.
subject_reps_vs_alleles_blastdb
Folder containing the BLASTp database for the rep vs rep analysis.
subject_reps_vs_alleles_blastdb.pdb
Position-specific Data Base file. Contains position-specific scoring matrices (PSSMs) used in PSI-BLAST searches.
subject_reps_vs_alleles_blastdb.phr
Protein Header Record file. Contains the header information for each sequence in the protein database.
subject_reps_vs_alleles_blastdb.pin
Protein Index file. Contains the index of the sequences in the protein database.
subject_reps_vs_alleles_blastdb.pog
Protein Organism Group file. Contains information about the taxonomic grouping of the sequences in the protein database.
subject_reps_vs_alleles_blastdb.pos
Protein Organism Sequence file. Contains the actual sequence data for the protein database.
subject_reps_vs_alleles_blastdb.pot
Protein Organism Taxonomy file. Contains taxonomic information for the sequences in the protein database.
subject_reps_vs_alleles_blastdb.psq
Protein Sequence Query file. Contains the sequence data in a format optimized for BLAST searches.
subject_reps_vs_alleles_blastdb.ptf
Protein Taxonomy File. Contains taxonomy information for the sequences in the protein database.
subject_reps_vs_alleles_blastdb.pto
Protein Taxonomy Organism file. Contains organism-specific taxonomy information for the sequences in the protein database.
blastp_results
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.
Query_Translation
Folder containing the query translation files.
query_translations_x.fasta
FASTA file containing the translation for the locus x.
query_translations_y.fasta
FASTA file containing the translation for the locus y.
query_translations_z.fasta
FASTA file containing the translation for the locus z.
...
All the other translation files.
Query_Translation_Rep
Folder containing the representative query translation files.
query_translations_x.fasta
FASTA file containing the translation for the locus x.
query_translations_y.fasta
FASTA file containing the translation for the locus y.
query_translations_z.fasta
FASTA file containing the translation for the locus z.
...
All the other translation files.
Subject_Translation
Folder containing the subject translation files.
subject_translations_x.fasta
FASTA file containing the translation for the locus x.
subject_translations_y.fasta
FASTA file containing the translation for the locus y.
subject_translations_z.fasta
FASTA file containing the translation for the locus z.
...
All the other translation files.
Subject_Translation_Rep
Folder containing the representative subject translation files.
subject_translations_x.fasta
FASTA file containing the translation for the locus x.
subject_translations_y.fasta
FASTA file containing the translation for the locus y.
subject_translations_z.fasta
FASTA file containing the translation for the locus z.
...
All the other translation files.
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 the locus z.
...
All the other TSV BLASTp for self-score results files.
**hashes_dna_matches.tsv**
TSV file with the matches from the DNA hashes analysis.
**hashes_prot_matches.tsv**
TSV file with the matches from the proteins hashes analysis.
**reps_vs_reps_matches.tsv**
TSV file with the matches from the reps vs reps Blastp analysis.
**reps_vs_alleles_matches.tsv**
TSV file with the matches from the reps vs alleles Blastp analysis.
**unmatched.tsv**
TSV file with the loci that were not matched analysis.
**Match_Schemas_Results.tsv**
TSV file containing the best BLAST matches for the query and subject schemas sorted by locus name. Also contains the final non-matched locus from both Query and Subject.