bin/Changelog.txt
bin/Docker/Dockerfile
bin/Docker/VERSION.txt
bin/Docker/build_docker.sh
bin/Docker/make_simg.sh
bin/Docker/push_docker.sh
bin/LICENSE.txt
bin/Makefile
bin/PerlLib/DelimParser.pm
bin/PerlLib/Fasta_reader.pm
bin/PerlLib/Fasta_retriever.pm
bin/PerlLib/GFF3_utils2.pm
bin/PerlLib/GTF.pm
bin/PerlLib/GTF_utils2.pm
bin/PerlLib/Gene_obj.pm
bin/PerlLib/Longest_orf.pm
bin/PerlLib/Nuc_translator.pm
bin/PerlLib/Overlap_piler.pm
bin/PerlLib/PWM.pm
bin/PerlLib/Pipeliner.pm
bin/PerlLib/Process_cmd.pm
bin/PerlLib/overlapping_nucs.ph
bin/README.md
bin/TransDecoder.LongOrfs
bin/TransDecoder.Predict
bin/__testing/Makefile
bin/__testing/__test.best_w_homology.expected
bin/__testing/__test.simplest.expected
bin/__testing/__test.single_best.expected
bin/__testing/__test.wBlastNPfam.expected
bin/__testing/blastp.outfmt6
bin/__testing/longest_orfs.cds.scores
bin/__testing/longest_orfs.gff3
bin/__testing/pfam.domtblout
bin/add_cds_to_gff.pl
bin/add_features.pl
bin/assign_class_code.pl
bin/blastp
bin/check_cds.pl
bin/combine_gene_protein_gff.pl
bin/compute_junction_counts.pl
bin/compute_junction_scores.pl
bin/compute_junction_scores_bed.pl
bin/convert_miniprot_gff.pl
bin/convert_trna.sh
bin/detect_readthrough_exons.pl
bin/detect_readthroughs.pl
bin/eviann.sh
bin/exonerate
bin/extract_utr_transcripts.pl
bin/ez_maker.sh
bin/filter_by_class_code.pl
bin/filter_by_local_abundance.pl
bin/filter_junctions.pl
bin/filter_unused_proteins.pl
bin/fix_palign_splice_sites.pl
bin/fix_splice_junctions.pl
bin/fix_suspect_introns.pl
bin/get_splice_sites.pl
bin/gffcompare
bin/gffread
bin/makeblastdb
bin/miniprot.tgz
bin/my_maker_functional_fasta
bin/my_maker_functional_gff
bin/notes
bin/reassign_transcripts.pl
bin/remove_readthrough_exons.pl
bin/samtools
bin/score_transcripts_with_hmms.pl
bin/stringtie
bin/tblToGFF.pl
bin/trmap
bin/ufasta
bin/util/PWM/README.md
bin/util/PWM/__deprecated/build_atgPWM.pl
bin/util/PWM/__deprecated/build_pwm.pl
bin/util/PWM/__deprecated/score_atgPWM.pl
bin/util/PWM/build_atgPWM_+-.pl
bin/util/PWM/compute_AUC.pl
bin/util/PWM/deplete_feature_noise.pl
bin/util/PWM/feature_scores_to_ROC.pl
bin/util/PWM/feature_scoring.+-.pl
bin/util/PWM/make_seqLogo.Rscript
bin/util/PWM/plot_ROC.Rscript
bin/util/PWM/simulate_feature_seq_from_PWM.pl
bin/util/__pwm_tests/cleanMe.sh
bin/util/__pwm_tests/longest_orfs.cds.top_longest_5000.nr80.gz
bin/util/__pwm_tests/pasa_assemblies.fasta.gz
bin/util/__pwm_tests/runMe.sh
bin/util/bin/.hidden
bin/util/cdna_alignment_orf_to_genome_orf.pl
bin/util/compute_base_probs.pl
bin/util/exclude_similar_proteins.pl
bin/util/fasta_prot_checker.pl
bin/util/ffindex_resume.pl
bin/util/gene_list_to_gff.pl
bin/util/get_FL_accs.pl
bin/util/get_longest_ORF_per_transcript.pl
bin/util/get_top_longest_fasta_entries.pl
bin/util/gff3_file_to_bed.pl
bin/util/gff3_file_to_proteins.pl
bin/util/gff3_gene_to_gtf_format.pl
bin/util/gtf_genome_to_cdna_fasta.pl
bin/util/gtf_to_alignment_gff3.pl
bin/util/gtf_to_bed.pl
bin/util/misc/__init__.py
bin/util/misc/get_FP_FN_scores.py
bin/util/misc/plot_indiv_seq_likelihood_profile.py
bin/util/misc/rpart_scores.Rscript
bin/util/misc/select_TD_orfs.py
bin/util/nr_ORFs_gff3.pl
bin/util/pfam_mpi.pbs
bin/util/pfam_runner.pl
bin/util/refine_gff3_group_iso_strip_utrs.pl
bin/util/refine_hexamer_scores.pl
bin/util/remove_eclipsed_ORFs.pl
bin/util/score_CDS_likelihood_all_6_frames.pl
bin/util/select_best_ORFs_per_transcript.pl
bin/util/seq_n_baseprobs_to_loglikelihood_vals.pl
bin/util/start_codon_refinement.pl
bin/util/train_start_PWM.pl
bin/util/uri_unescape.pl
