%FILES%
usr/
usr/lib/
usr/lib/ProtHint/
usr/lib/ProtHint/bin/
usr/lib/ProtHint/bin/cds_with_upstream_support.py
usr/lib/ProtHint/bin/combine_gff_records.pl
usr/lib/ProtHint/bin/count_cds_overlaps.py
usr/lib/ProtHint/bin/flag_top_proteins.py
usr/lib/ProtHint/bin/gff_from_region_to_contig.pl
usr/lib/ProtHint/bin/make_chains.py
usr/lib/ProtHint/bin/nucseq_for_selected_genes.pl
usr/lib/ProtHint/bin/print_high_confidence.py
usr/lib/ProtHint/bin/print_longest_isoform.py
usr/lib/ProtHint/bin/proteins_from_gtf.pl
usr/lib/ProtHint/bin/prothint.py
usr/lib/ProtHint/bin/prothint2augustus.py
usr/lib/ProtHint/bin/run_spliced_alignment.pl
usr/lib/ProtHint/bin/run_spliced_alignment_pbs.pl
usr/lib/ProtHint/bin/select_best_proteins.py
usr/lib/ProtHint/bin/select_for_next_iteration.py
usr/lib/ProtHint/bin/spalnBatch.sh
usr/lib/ProtHint/bin/spaln_to_gff.py
usr/lib/ProtHint/dependencies/
usr/lib/ProtHint/dependencies/GeneMarkES/
usr/lib/ProtHint/dependencies/blosum62.csv
usr/lib/ProtHint/dependencies/diamond
usr/lib/ProtHint/dependencies/log_reg_prothints.pl
usr/lib/ProtHint/dependencies/probuild
usr/lib/ProtHint/dependencies/spaln
usr/lib/ProtHint/dependencies/spaln_boundary_scorer
usr/lib/ProtHint/dependencies/spaln_table/
usr/lib/ProtHint/dependencies/spaln_table/AlnParam
usr/lib/ProtHint/dependencies/spaln_table/Branch
usr/lib/ProtHint/dependencies/spaln_table/CodePotTab
usr/lib/ProtHint/dependencies/spaln_table/Hoxd55
usr/lib/ProtHint/dependencies/spaln_table/Hoxd70
usr/lib/ProtHint/dependencies/spaln_table/IldModel.txt
usr/lib/ProtHint/dependencies/spaln_table/Intron53
usr/lib/ProtHint/dependencies/spaln_table/IpStat.txt
usr/lib/ProtHint/dependencies/spaln_table/Splice3
usr/lib/ProtHint/dependencies/spaln_table/Splice5
usr/lib/ProtHint/dependencies/spaln_table/StrandPhrase
usr/lib/ProtHint/dependencies/spaln_table/TransInit
usr/lib/ProtHint/dependencies/spaln_table/TransTerm
usr/lib/ProtHint/dependencies/spaln_table/blosum62
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usr/lib/ProtHint/dependencies/spaln_table/hydro
usr/lib/ProtHint/dependencies/spaln_table/mdm_cmp
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usr/lib/ProtHint/dependencies/spaln_table/miqs
usr/lib/ProtHint/dependencies/spaln_table/reducedaa
usr/lib/ProtHint/dependencies/spaln_table/renzyme
usr/lib/ProtHint/dependencies/spaln_table/sas_mymt
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usr/lib/ProtHint/dependencies/spaln_table/sas_ngmt
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usr/lib/ProtHint/dependencies/spaln_table/vtml160
usr/lib/ProtHint/dependencies/spaln_table/vtml200
usr/lib/ProtHint/dependencies/spaln_table/vtml250
usr/lib/ProtHint/example/
usr/lib/ProtHint/example/README.md
usr/lib/ProtHint/example/input/
usr/lib/ProtHint/example/input/genemark.gtf
usr/lib/ProtHint/example/input/genome.fasta
usr/lib/ProtHint/example/input/proteins.fasta
usr/lib/ProtHint/example/output/
usr/lib/ProtHint/example/output/Spaln/
usr/lib/ProtHint/example/output/Spaln/spaln.gff
usr/lib/ProtHint/example/output/cmd.log
usr/lib/ProtHint/example/output/diamond/
usr/lib/ProtHint/example/output/diamond/diamond.out
usr/lib/ProtHint/example/output/diamond/diamond_db.dmnd
usr/lib/ProtHint/example/output/evidence.gff
usr/lib/ProtHint/example/output/gene_stat.yaml
usr/lib/ProtHint/example/output/nuc.fasta
usr/lib/ProtHint/example/output/prothint.gff
usr/lib/ProtHint/example/output/prothint_augustus.gff
usr/lib/ProtHint/example/output/seed_proteins.faa
usr/lib/ProtHint/example/output/top_chains.gff
usr/share/
usr/share/licenses/
usr/share/licenses/ProtHint/
usr/share/licenses/ProtHint/LICENSE
