bin/TransDecoder.LongOrfs
bin/TransDecoder.Predict
bin/cdna_alignment_orf_to_genome_orf.pl
bin/compute_base_probs.pl
bin/exclude_similar_proteins.pl
bin/fasta_prot_checker.pl
bin/ffindex_resume.pl
bin/gene_list_to_gff.pl
bin/get_FL_accs.pl
bin/get_longest_ORF_per_transcript.pl
bin/get_top_longest_fasta_entries.pl
bin/gff3_file_to_bed.pl
bin/gff3_file_to_proteins.pl
bin/gff3_gene_to_gtf_format.pl
bin/gtf_genome_to_cdna_fasta.pl
bin/gtf_to_alignment_gff3.pl
bin/gtf_to_bed.pl
bin/nr_ORFs_gff3.pl
bin/pfam_runner.pl
bin/refine_gff3_group_iso_strip_utrs.pl
bin/refine_hexamer_scores.pl
bin/remove_eclipsed_ORFs.pl
bin/score_CDS_likelihood_all_6_frames.pl
bin/select_best_ORFs_per_transcript.pl
bin/seq_n_baseprobs_to_loglikelihood_vals.pl
bin/start_codon_refinement.pl
bin/train_start_PWM.pl
bin/uri_unescape.pl
opt/transdecoder/.gitmodules
opt/transdecoder/Changelog.txt
opt/transdecoder/LICENSE.txt
opt/transdecoder/Makefile
opt/transdecoder/PerlLib/DelimParser.pm
opt/transdecoder/PerlLib/Fasta_reader.pm
opt/transdecoder/PerlLib/Fasta_retriever.pm
opt/transdecoder/PerlLib/GFF3_utils2.pm
opt/transdecoder/PerlLib/GTF.pm
opt/transdecoder/PerlLib/GTF_utils2.pm
opt/transdecoder/PerlLib/Gene_obj.pm
opt/transdecoder/PerlLib/Longest_orf.pm
opt/transdecoder/PerlLib/Nuc_translator.pm
opt/transdecoder/PerlLib/Overlap_piler.pm
opt/transdecoder/PerlLib/PWM.pm
opt/transdecoder/PerlLib/Pipeliner.pm
opt/transdecoder/PerlLib/Process_cmd.pm
opt/transdecoder/PerlLib/overlapping_nucs.ph
opt/transdecoder/README.md
opt/transdecoder/TransDecoder.LongOrfs
opt/transdecoder/TransDecoder.Predict
opt/transdecoder/__testing/Makefile
opt/transdecoder/__testing/__test.best_w_homology.expected
opt/transdecoder/__testing/__test.simplest.expected
opt/transdecoder/__testing/__test.single_best.expected
opt/transdecoder/__testing/__test.wBlastNPfam.expected
opt/transdecoder/__testing/blastp.outfmt6
opt/transdecoder/__testing/longest_orfs.cds.scores
opt/transdecoder/__testing/longest_orfs.gff3
opt/transdecoder/__testing/pfam.domtblout
opt/transdecoder/build_env_setup.sh
opt/transdecoder/conda_build.sh
opt/transdecoder/metadata_conda_debug.yaml
opt/transdecoder/notes
opt/transdecoder/sample_data/Makefile
opt/transdecoder/sample_data/README
opt/transdecoder/sample_data/README.md
opt/transdecoder/sample_data/cufflinks_example/Makefile
opt/transdecoder/sample_data/cufflinks_example/cleanme.pl
opt/transdecoder/sample_data/cufflinks_example/mini_Pfam-A.hmm.gz
opt/transdecoder/sample_data/cufflinks_example/mini_sprot.db.pep.gz
opt/transdecoder/sample_data/cufflinks_example/runMe.sh
opt/transdecoder/sample_data/cufflinks_example/test.genome.fasta.gz
opt/transdecoder/sample_data/cufflinks_example/test.tophat.sam.gz
opt/transdecoder/sample_data/cufflinks_example/transcripts.gtf.gz
opt/transdecoder/sample_data/pasa_example/Makefile
opt/transdecoder/sample_data/pasa_example/cleanme.pl
opt/transdecoder/sample_data/pasa_example/genome.fasta.gz
opt/transdecoder/sample_data/pasa_example/pasa_assemblies.fasta.gz
opt/transdecoder/sample_data/pasa_example/pasa_assemblies.gff3.gz
opt/transdecoder/sample_data/pasa_example/pasa_assemblies_described.txt.gz
opt/transdecoder/sample_data/pasa_example/runMe.sh
opt/transdecoder/sample_data/simple_transcriptome_target/Makefile
opt/transdecoder/sample_data/simple_transcriptome_target/Trinity.fasta.gz
opt/transdecoder/sample_data/simple_transcriptome_target/cleanme.pl
opt/transdecoder/sample_data/simple_transcriptome_target/genome_alignments.gmap.gff3.gz
opt/transdecoder/sample_data/simple_transcriptome_target/runMe.sh
opt/transdecoder/sample_data/stringtie_example/Makefile
opt/transdecoder/sample_data/stringtie_example/cleanme.pl
opt/transdecoder/sample_data/stringtie_example/runMe.sh
opt/transdecoder/sample_data/stringtie_example/stringtie_merged.gtf
opt/transdecoder/sample_data/stringtie_example/stringtie_merged.transcripts.fasta
opt/transdecoder/sample_data/supertranscripts_example/Makefile
opt/transdecoder/sample_data/supertranscripts_example/cleanme.pl
opt/transdecoder/sample_data/supertranscripts_example/runMe.sh
opt/transdecoder/sample_data/supertranscripts_example/supertranscripts.fasta
opt/transdecoder/sample_data/supertranscripts_example/supertranscripts.gtf
opt/transdecoder/util/PWM/README.md
opt/transdecoder/util/PWM/__deprecated/build_atgPWM.pl
opt/transdecoder/util/PWM/__deprecated/build_pwm.pl
opt/transdecoder/util/PWM/__deprecated/score_atgPWM.pl
opt/transdecoder/util/PWM/build_atgPWM_+-.pl
opt/transdecoder/util/PWM/compute_AUC.pl
opt/transdecoder/util/PWM/deplete_feature_noise.pl
opt/transdecoder/util/PWM/feature_scores_to_ROC.pl
opt/transdecoder/util/PWM/feature_scoring.+-.pl
opt/transdecoder/util/PWM/make_seqLogo.Rscript
opt/transdecoder/util/PWM/plot_ROC.Rscript
opt/transdecoder/util/PWM/simulate_feature_seq_from_PWM.pl
opt/transdecoder/util/__pwm_tests/cleanMe.sh
opt/transdecoder/util/__pwm_tests/longest_orfs.cds.top_longest_5000.nr80.gz
opt/transdecoder/util/__pwm_tests/pasa_assemblies.fasta.gz
opt/transdecoder/util/__pwm_tests/runMe.sh
opt/transdecoder/util/bin/.hidden
opt/transdecoder/util/cdna_alignment_orf_to_genome_orf.pl
opt/transdecoder/util/compute_base_probs.pl
opt/transdecoder/util/exclude_similar_proteins.pl
opt/transdecoder/util/fasta_prot_checker.pl
opt/transdecoder/util/ffindex_resume.pl
opt/transdecoder/util/gene_list_to_gff.pl
opt/transdecoder/util/get_FL_accs.pl
opt/transdecoder/util/get_longest_ORF_per_transcript.pl
opt/transdecoder/util/get_top_longest_fasta_entries.pl
opt/transdecoder/util/gff3_file_to_bed.pl
opt/transdecoder/util/gff3_file_to_proteins.pl
opt/transdecoder/util/gff3_gene_to_gtf_format.pl
opt/transdecoder/util/gtf_genome_to_cdna_fasta.pl
opt/transdecoder/util/gtf_to_alignment_gff3.pl
opt/transdecoder/util/gtf_to_bed.pl
opt/transdecoder/util/misc/__init__.py
opt/transdecoder/util/misc/get_FP_FN_scores.py
opt/transdecoder/util/misc/plot_indiv_seq_likelihood_profile.py
opt/transdecoder/util/misc/rpart_scores.Rscript
opt/transdecoder/util/misc/select_TD_orfs.py
opt/transdecoder/util/nr_ORFs_gff3.pl
opt/transdecoder/util/pfam_mpi.pbs
opt/transdecoder/util/pfam_runner.pl
opt/transdecoder/util/refine_gff3_group_iso_strip_utrs.pl
opt/transdecoder/util/refine_hexamer_scores.pl
opt/transdecoder/util/remove_eclipsed_ORFs.pl
opt/transdecoder/util/score_CDS_likelihood_all_6_frames.pl
opt/transdecoder/util/select_best_ORFs_per_transcript.pl
opt/transdecoder/util/seq_n_baseprobs_to_loglikelihood_vals.pl
opt/transdecoder/util/start_codon_refinement.pl
opt/transdecoder/util/train_start_PWM.pl
opt/transdecoder/util/uri_unescape.pl
