@comment $NetBSD$
bin/Trinity
libexec/trinity/Butterfly/Butterfly.jar
libexec/trinity/Chrysalis/BreakTransByPairs
libexec/trinity/Chrysalis/checkLock
libexec/trinity/Chrysalis/Chrysalis
libexec/trinity/Chrysalis/GraphFromFasta
libexec/trinity/Chrysalis/IsoformAugment
libexec/trinity/Chrysalis/JoinTransByPairs
libexec/trinity/Chrysalis/QuantifyGraph
libexec/trinity/Chrysalis/ReadsToComponents.pl
libexec/trinity/Chrysalis/ReadsToTranscripts
libexec/trinity/Chrysalis/RunButterfly
libexec/trinity/Chrysalis/TranscriptomeFromVaryK
libexec/trinity/Inchworm/bin/cigar_tweaker
libexec/trinity/Inchworm/bin/FastaToDeBruijn
libexec/trinity/Inchworm/bin/fastaToKmerCoverageStats
libexec/trinity/Inchworm/bin/inchworm
libexec/trinity/Inchworm/bin/pull_reads_with_kmers
libexec/trinity/PerlLib/Ascii_genome_illustrator.pm
libexec/trinity/PerlLib/BED_utils.pm
libexec/trinity/PerlLib/BHStats.pm
libexec/trinity/PerlLib/cache_completed_LSF_cmds
libexec/trinity/PerlLib/cache_completed_SGE_cmds
libexec/trinity/PerlLib/CanvasXpress/Heatmap.pm
libexec/trinity/PerlLib/CDNA/Alignment_segment.pm
libexec/trinity/PerlLib/CDNA/Alternative_splice_comparer.pm
libexec/trinity/PerlLib/CDNA/CDNA_alignment.pm
libexec/trinity/PerlLib/CDNA/CDNA_stitcher.pm
libexec/trinity/PerlLib/CDNA/Gene_obj_alignment_assembler.pm
libexec/trinity/PerlLib/CDNA/Genome_based_cDNA_assembler.pm
libexec/trinity/PerlLib/CDNA/Genome_based_cDNA_graph_assembler.pm
libexec/trinity/PerlLib/CDNA/Overlap_assembler.pm
libexec/trinity/PerlLib/CDNA/PASA_alignment_assembler.pm
libexec/trinity/PerlLib/CDNA/Splice_graph_assembler.pm
libexec/trinity/PerlLib/CIGAR.pm
libexec/trinity/PerlLib/CMD_processor.pm
libexec/trinity/PerlLib/cmds_for_parafly.txt
libexec/trinity/PerlLib/cmds_for_parafly.txt.completed
libexec/trinity/PerlLib/ColorGradient.pm
libexec/trinity/PerlLib/EM.pm
libexec/trinity/PerlLib/Exons_to_geneobj.pm
libexec/trinity/PerlLib/FailedCommands
libexec/trinity/PerlLib/Fasta_reader.pm
libexec/trinity/PerlLib/Fasta_retriever.pm
libexec/trinity/PerlLib/Fastq_reader.pm
libexec/trinity/PerlLib/Gene_obj_indexer.pm
libexec/trinity/PerlLib/Gene_obj.pm
libexec/trinity/PerlLib/GFF3_alignment_utils.pm
libexec/trinity/PerlLib/GFF3_utils.pm
libexec/trinity/PerlLib/GFF_maker.pm
libexec/trinity/PerlLib/GTF.pm
libexec/trinity/PerlLib/GTF_utils.pm
libexec/trinity/PerlLib/HTC/Base_handler.pm
libexec/trinity/PerlLib/HTC/FarmIt.pm
libexec/trinity/PerlLib/HTC/GridRunner.pm
libexec/trinity/PerlLib/HTC/LSF_handler.pm
libexec/trinity/PerlLib/HTC/SGE_handler.pm
libexec/trinity/PerlLib/HTC/SLURM_handler.pm
libexec/trinity/PerlLib/J14349.S0.sh.e7297570
libexec/trinity/PerlLib/J14349.S0.sh.o7297570
libexec/trinity/PerlLib/J14349.S10.sh.e7297580
libexec/trinity/PerlLib/J14349.S10.sh.o7297580
libexec/trinity/PerlLib/J14349.S1.sh.e7297571
libexec/trinity/PerlLib/J14349.S1.sh.o7297571
libexec/trinity/PerlLib/J14349.S2.sh.e7297572
libexec/trinity/PerlLib/J14349.S2.sh.o7297572
libexec/trinity/PerlLib/J14349.S3.sh.e7297573
libexec/trinity/PerlLib/J14349.S3.sh.o7297573
libexec/trinity/PerlLib/J14349.S4.sh.e7297574
libexec/trinity/PerlLib/J14349.S4.sh.o7297574
libexec/trinity/PerlLib/J14349.S5.sh.e7297575
libexec/trinity/PerlLib/J14349.S5.sh.o7297575
libexec/trinity/PerlLib/J14349.S6.sh.e7297576
libexec/trinity/PerlLib/J14349.S6.sh.o7297576
libexec/trinity/PerlLib/J14349.S7.sh.e7297577
libexec/trinity/PerlLib/J14349.S7.sh.o7297577
libexec/trinity/PerlLib/J14349.S8.sh.e7297578
libexec/trinity/PerlLib/J14349.S8.sh.o7297578
libexec/trinity/PerlLib/J14349.S9.sh.e7297579
libexec/trinity/PerlLib/J14349.S9.sh.o7297579
libexec/trinity/PerlLib/KmerGraphLib/AlignGraph.pm
libexec/trinity/PerlLib/KmerGraphLib/AlignNode.pm
libexec/trinity/PerlLib/KmerGraphLib/GenericGraph.pm
libexec/trinity/PerlLib/KmerGraphLib/GenericNode.pm
libexec/trinity/PerlLib/KmerGraphLib/KmerGraph.pm
libexec/trinity/PerlLib/KmerGraphLib/KmerNode.pm
libexec/trinity/PerlLib/KmerGraphLib/ReadCoverageGraph.pm
libexec/trinity/PerlLib/KmerGraphLib/ReadCoverageNode.pm
libexec/trinity/PerlLib/KmerGraphLib/ReadManager.pm
libexec/trinity/PerlLib/KmerGraphLib/ReadTracker.pm
libexec/trinity/PerlLib/KmerGraphLib/SAM_entry.pm
libexec/trinity/PerlLib/KmerGraphLib/SAM_reader.pm
libexec/trinity/PerlLib/KmerGraphLib/SAM_to_AlignGraph.pm
libexec/trinity/PerlLib/KmerGraphLib/StringGraph.pm
libexec/trinity/PerlLib/KmerGraphLib/StringNode.pm
libexec/trinity/PerlLib/Ktree.pm
libexec/trinity/PerlLib/Longest_orf.pm
libexec/trinity/PerlLib/Nuc_translator.pm
libexec/trinity/PerlLib/Overlap_info.pm
libexec/trinity/PerlLib/Overlap_piler.pm
libexec/trinity/PerlLib/overlapping_nucs.ph
libexec/trinity/PerlLib/PSL_parser.pm
libexec/trinity/PerlLib/SAM_entry.pm
libexec/trinity/PerlLib/SAM_reader.pm
libexec/trinity/PerlLib/Simulate/Uniform_Read_Generator.pm
libexec/trinity/PerlLib/SingleLinkageClusterer.pm
libexec/trinity/PerlLib/test_Fasta_retriever.pl
libexec/trinity/PerlLib/test_htc_gridrunner_LSF.pl
libexec/trinity/PerlLib/test_htc_gridrunner_SGE.pl
libexec/trinity/PerlLib/Thread_helper.pm
libexec/trinity/PerlLib/TiedHash.pm
libexec/trinity/PerlLib/VCF_parser.pm
libexec/trinity/PerlLib/WigParser.pm
libexec/trinity/trinity-plugins/collectl/bin/client.pl
libexec/trinity/trinity-plugins/collectl/bin/col2tlviz.pl
libexec/trinity/trinity-plugins/collectl/bin/collectl
libexec/trinity/trinity-plugins/collectl/bin/collectl.conf
libexec/trinity/trinity-plugins/collectl/bin/envrules.std
libexec/trinity/trinity-plugins/collectl/bin/formatit.ph
libexec/trinity/trinity-plugins/collectl/bin/gexpr.ph
libexec/trinity/trinity-plugins/collectl/bin/graphite.ph
libexec/trinity/trinity-plugins/collectl/bin/hello.ph
libexec/trinity/trinity-plugins/collectl/bin/lexpr.ph
libexec/trinity/trinity-plugins/collectl/bin/make_data_files.sh
libexec/trinity/trinity-plugins/collectl/bin/misc.ph
libexec/trinity/trinity-plugins/collectl/bin/nvidia.ph
libexec/trinity/trinity-plugins/collectl/bin/plot.sh
libexec/trinity/trinity-plugins/collectl/bin/proctree.ph
libexec/trinity/trinity-plugins/collectl/bin/sexpr.ph
libexec/trinity/trinity-plugins/collectl/bin/timetable.sh
libexec/trinity/trinity-plugins/collectl/bin/UNINSTALL
libexec/trinity/trinity-plugins/collectl/bin/vmstat.ph
libexec/trinity/trinity-plugins/coreutils/bin/sort
libexec/trinity/trinity-plugins/fastool/fastool
libexec/trinity/trinity-plugins/parafly/bin/ParaFly
libexec/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq2-PE.fa
libexec/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq2-SE.fa
libexec/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa
libexec/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-SE.fa
libexec/trinity/trinity-plugins/Trimmomatic/trimmomatic-0.30.jar
libexec/trinity/trinity-plugins/Trimmomatic/trimmomatic.jar
libexec/trinity/util/abundance_estimates_to_matrix.pl
libexec/trinity/util/align_and_estimate_abundance.pl
libexec/trinity/util/analyze_blastPlus_topHit_coverage.pl
libexec/trinity/util/bowtie_PE_separate_then_join.pl
libexec/trinity/util/deprecated/alignReads.pl
libexec/trinity/util/deprecated/annot_genome_SAM_to_transcript_FPKM_simple.pl
libexec/trinity/util/deprecated/annot_genome_SAM_to_transcriptome_SAM.pl
libexec/trinity/util/deprecated/blastn_illumina_to_SAM.pl
libexec/trinity/util/deprecated/cigar_tweaker.pl
libexec/trinity/util/deprecated/cmd_process_forker.pl
libexec/trinity/util/deprecated/csfastX_to_defastA.pl
libexec/trinity/util/deprecated/distribute_sam_aligned_reads.pl
libexec/trinity/util/deprecated/eXpress_util/filter_contigs.py
libexec/trinity/util/deprecated/eXpress_util/merge_eXpress_frag_counts_single_table.pl
libexec/trinity/util/deprecated/eXpress_util/run_eXpress_align_n_estimate.pl
libexec/trinity/util/deprecated/eXpress_util/usage.txt
libexec/trinity/util/deprecated/eXpress_util/use_express.py
libexec/trinity/util/deprecated/fasta_to_deBruijn_graph.pl
libexec/trinity/util/deprecated/PairPathsToGraphDot.pl
libexec/trinity/util/deprecated/purge_dir.pl
libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_frag_counts_single_table.pl
libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_output_to_matrix.pl
libexec/trinity/util/deprecated/RSEM_util/Nx_rsem_to_table.pl
libexec/trinity/util/deprecated/RSEM_util/run_RSEM_align_n_estimate.pl
libexec/trinity/util/deprecated/run_AllpathsLG_error_correction.pl
libexec/trinity/util/deprecated/sort_fasta.sh
libexec/trinity/util/deprecated/write_inchworm_cmds.pl
libexec/trinity/util/fasta_tool
libexec/trinity/util/filter_fasta_by_rsem_values.pl
libexec/trinity/util/HTC_helpers/bsub_fasta_bin_cmd_processor.pl
libexec/trinity/util/HTC_helpers/htc_bin_blastPlus.pl
libexec/trinity/util/HTC_helpers/run_cmds_on_grid.pl
libexec/trinity/util/insilico_read_normalization.pl
libexec/trinity/util/ladeda.pl
libexec/trinity/util/misc/acc_list_to_fasta_entries.pl
libexec/trinity/util/misc/alexie_analyze_blast.pl
libexec/trinity/util/misc/allele_simulator.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.extract_OS.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.org_matrix.pl
libexec/trinity/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
libexec/trinity/util/misc/average.pl
libexec/trinity/util/misc/blastn_wrapper.pl
libexec/trinity/util/misc/BLAT_to_SAM.pl
libexec/trinity/util/misc/blat_util/blat_sam_add_reads2.pl
libexec/trinity/util/misc/blat_util/blat_top_hit_extractor.pl
libexec/trinity/util/misc/blat_util/blat_to_sam.pl
libexec/trinity/util/misc/blat_util/process_BLAT_alignments.pl
libexec/trinity/util/misc/blat_util/pslx_to_gff3.pl
libexec/trinity/util/misc/blat_util/run_BLAT_shortReads.pl
libexec/trinity/util/misc/blat_util/top_blat_sam_extractor.pl
libexec/trinity/util/misc/ButterflyFastaToGraphDot.pl
libexec/trinity/util/misc/capture_orig_n_unmapped_reads.pl
libexec/trinity/util/misc/cat_require_newlines.pl
libexec/trinity/util/misc/cdna_fasta_file_to_transcript_gtf.pl
libexec/trinity/util/misc/check_fastQ_pair_ordering.pl
libexec/trinity/util/misc/chrys_graph_to_dot.pl
libexec/trinity/util/misc/combined_nameSorted_to_dup_pairs_removed.pl
libexec/trinity/util/misc/compare_bflies.pl
libexec/trinity/util/misc/component_to_graph_dot.pl
libexec/trinity/util/misc/convert_fasta_identifiers_for_FL_analysis.pl
libexec/trinity/util/misc/count_features_given_MIN_FPKM_threshold.pl
libexec/trinity/util/misc/count_N50_given_MIN_FPKM_threshold.pl
libexec/trinity/util/misc/count_number_fasta_seqs.pl
libexec/trinity/util/misc/count_trans_per_component.pl
libexec/trinity/util/misc/decode_SAM_flag_value.pl
libexec/trinity/util/misc/describe_SAM_read_flag_info.pl
libexec/trinity/util/misc/examine_iworm_FL_across_threads.pl
libexec/trinity/util/misc/examine_weldmer_halves.pl
libexec/trinity/util/misc/extract_fastQ_pairings.pl
libexec/trinity/util/misc/fasta_file_reformatter.pl
libexec/trinity/util/misc/fasta_filter_by_min_length.pl
libexec/trinity/util/misc/fasta_remove_duplicates.pl
libexec/trinity/util/misc/fasta_to_cmd_generator.pl
libexec/trinity/util/misc/fasta_write_sense_n_anti.pl
libexec/trinity/util/misc/fastQ_append_acc.pl
libexec/trinity/util/misc/fastq_cleaner.pl
libexec/trinity/util/misc/fastq_interleave_pairs.pl
libexec/trinity/util/misc/fastq_merge_sorted_tab_lists.pl
libexec/trinity/util/misc/fastQ_rand_subset.pl
libexec/trinity/util/misc/fastq_stats.pl
libexec/trinity/util/misc/fastQ_top_N_records.pl
libexec/trinity/util/misc/fastq_unweave_pairs.pl
libexec/trinity/util/misc/frag_boundary_to_wig.pl
libexec/trinity/util/misc/frag_to_bed.pl
libexec/trinity/util/misc/gene_gff3_to_introns.pl
libexec/trinity/util/misc/get_path_nodes_from_fasta.pl
libexec/trinity/util/misc/gff3_file_to_cdna.pl
libexec/trinity/util/misc/gff3_file_utr_coverage_trimmer.pl
libexec/trinity/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
libexec/trinity/util/misc/gff3_to_genome_feature_base_encoding.pl
libexec/trinity/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl
libexec/trinity/util/misc/gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
libexec/trinity/util/misc/gmap_gff3_to_percent_length_stats.pl
libexec/trinity/util/misc/gmap_native_to_format_converter.pl
libexec/trinity/util/misc/gtf_to_bed_format.pl
libexec/trinity/util/misc/gtf_to_introns.pl
libexec/trinity/util/misc/HiCpipe_nameSortedSam_to_raw.pl
libexec/trinity/util/misc/hicpipe_raw_converter.pl
libexec/trinity/util/misc/identify_distal_isoform_variations.pl
libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.all.txt
libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.NormMaxKCov50.txt
libexec/trinity/util/misc/insilico_norm_kmer_hists/plot_me.R
libexec/trinity/util/misc/insilico_norm_kmer_hists/result.pdf
libexec/trinity/util/misc/jaccard_sam_pair_refiner.pl
libexec/trinity/util/misc/join_any.pl
libexec/trinity/util/misc/join_by_left_col.pl
libexec/trinity/util/misc/join_expr_vals_single_table.pl
libexec/trinity/util/misc/kmer_counter.pl
libexec/trinity/util/misc/m8_blastclust.pl
libexec/trinity/util/misc/map_gtf_transcripts_to_genome_annots.pl
libexec/trinity/util/misc/merge_blast_n_rsem_results.pl
libexec/trinity/util/misc/merge_rsem_n_express_for_compare.pl
libexec/trinity/util/misc/Monarch
libexec/trinity/util/misc/N50.pl
libexec/trinity/util/misc/nameSorted_SAM_to_FastQ.pl
libexec/trinity/util/misc/organize_data_table_by_trinity_component.pl
libexec/trinity/util/misc/pairwise_kmer_content_comparer.pl
libexec/trinity/util/misc/PerlLib/SegmentGraph.pm
libexec/trinity/util/misc/plot_expressed_gene_dist.pl
libexec/trinity/util/misc/print_kmers.pl
libexec/trinity/util/misc/print.pl
libexec/trinity/util/misc/prop_pair_sam_refiner.pl
libexec/trinity/util/misc/remove_cntrl_chars.pl
libexec/trinity/util/misc/row_to_column.pl
libexec/trinity/util/misc/run_bwasw_trinity.pl
libexec/trinity/util/misc/run_HiCpipe_bowtie.pl
libexec/trinity/util/misc/run_jellyfish.pl
libexec/trinity/util/misc/run_read_simulator_per_fasta_entry.pl
libexec/trinity/util/misc/run_read_simulator_per_gene.pl
libexec/trinity/util/misc/run_TOPHAT.pl
libexec/trinity/util/misc/run_trimmomatic_qual_trimming.pl
libexec/trinity/util/misc/SAM_coordsorted_max_reads_per_position.pl
libexec/trinity/util/misc/SAM_intron_extractor.pl
libexec/trinity/util/misc/SAM_show_alignment.pl
libexec/trinity/util/misc/SAM_show_alignment.summarize_stats.pl
libexec/trinity/util/misc/SAM_sortAny_to_count_stats.pl
libexec/trinity/util/misc/SAM_to_bed.pl
libexec/trinity/util/misc/SAM_to_fasta.pl
libexec/trinity/util/misc/SAM_toString.pl
libexec/trinity/util/misc/shuffle.pl
libexec/trinity/util/misc/simulate_illuminaPE_from_transcripts.pl
libexec/trinity/util/misc/sort_fastq.pl
libexec/trinity/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
libexec/trinity/util/misc/splice_path_analysis/assess_intron_path_sensitivity.summarizer.pl
libexec/trinity/util/misc/splice_path_analysis/diff_splice_paths.pl
libexec/trinity/util/misc/splice_path_analysis/intron_barcharter.pl
libexec/trinity/util/misc/SRA_to_fastq.notes
libexec/trinity/util/misc/SRA_to_fastq.pl
libexec/trinity/util/misc/strip_fasta_header.pl
libexec/trinity/util/misc/tab_to_fasta.pl
libexec/trinity/util/misc/tab_to_fastQ.pl
libexec/trinity/util/misc/tblastn_wrapper.pl
libexec/trinity/util/misc/testUnlimitStacksize.pl
libexec/trinity/util/misc/TophatCufflinksWrapper.pl
libexec/trinity/util/misc/transcript_coverage_UTR_trimmer.pl
libexec/trinity/util/misc/transcript_fasta_to_ORF_pics.pl
libexec/trinity/util/misc/transcript_gff3_to_bed.pl
libexec/trinity/util/misc/transdecoder_pep_to_false_fusion_finder.pl
libexec/trinity/util/misc/trinity_component_distribution.pl
libexec/trinity/util/PBS/N50stats.pl
libexec/trinity/util/PBS/pbs_check.pl
libexec/trinity/util/PBS/README
libexec/trinity/util/PBS/TRINITY.CONFIG.template
libexec/trinity/util/PBS/trinity_kill.pl
libexec/trinity/util/PBS/trinity_kill.sh
libexec/trinity/util/PBS/trinity_pbs.cont
libexec/trinity/util/PBS/trinity_pbs.header
libexec/trinity/util/PBS/trinity_pbs.p1
libexec/trinity/util/PBS/trinity_pbs.p2
libexec/trinity/util/PBS/trinity_pbs.p3
libexec/trinity/util/PBS/trinity_pbs.p4a
libexec/trinity/util/PBS/trinity_pbs.p4b
libexec/trinity/util/PBS/trinity_pbs.p5b
libexec/trinity/util/PBS/trinity_pbs.sh
libexec/trinity/util/retrieve_sequences_from_fasta.pl
libexec/trinity/util/R/expression_analysis_lib.R
libexec/trinity/util/R/get_Poisson_conf_intervals.R
libexec/trinity/util/R/noiseq.r
libexec/trinity/util/run_Trinity_edgeR_pipeline.pl
libexec/trinity/util/SAM_nameSorted_to_uniq_count_stats.pl
libexec/trinity/util/support_scripts/define_coverage_partitions.pl
libexec/trinity/util/support_scripts/define_SAM_coverage_partitions2.pl
libexec/trinity/util/support_scripts/ExitTester.jar
libexec/trinity/util/support_scripts/eXpress_trans_to_gene_results.pl
libexec/trinity/util/support_scripts/extract_reads_per_partition.pl
libexec/trinity/util/support_scripts/fasta_to_tab.pl
libexec/trinity/util/support_scripts/fastQ_to_fastA.pl
libexec/trinity/util/support_scripts/fastQ_to_tab.pl
libexec/trinity/util/support_scripts/fragment_coverage_writer.pl
libexec/trinity/util/support_scripts/get_Trinity_gene_to_trans_map.pl
libexec/trinity/util/support_scripts/GG_trinity_accession_incrementer.pl
libexec/trinity/util/support_scripts/GG_write_trinity_cmds.pl
libexec/trinity/util/support_scripts/inchworm_transcript_splitter.pl
libexec/trinity/util/support_scripts/install_tests.sh
libexec/trinity/util/support_scripts/jaccard_fasta_clipper.pl
libexec/trinity/util/support_scripts/jaccard_wig_clipper.pl
libexec/trinity/util/support_scripts/join_partitions_within_range.pl
libexec/trinity/util/support_scripts/merge_left_right_nameSorted_SAMs.pl
libexec/trinity/util/support_scripts/nbkc_merge_left_right_stats.pl
libexec/trinity/util/support_scripts/nbkc_normalize.pl
libexec/trinity/util/support_scripts/ordered_fragment_coords_to_jaccard.pl
libexec/trinity/util/support_scripts/partition_chrysalis_graphs_n_reads.pl
libexec/trinity/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
libexec/trinity/util/support_scripts/print_butterfly_assemblies.pl
libexec/trinity/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
libexec/trinity/util/support_scripts/revcomp_fasta.pl
libexec/trinity/util/support_scripts/run_TMM_scale_matrix.pl
libexec/trinity/util/support_scripts/run_UpperQuartileNormalization_matrix.pl
libexec/trinity/util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
libexec/trinity/util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
libexec/trinity/util/support_scripts/SAM_extract_properly_mapped_pairs.pl
libexec/trinity/util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
libexec/trinity/util/support_scripts/SAM_filter_out_unmapped_reads.pl
libexec/trinity/util/support_scripts/SAM_ordered_pair_jaccard.pl
libexec/trinity/util/support_scripts/SAM_set_transcribed_orient_info.pl
libexec/trinity/util/support_scripts/SAM_strand_separator.pl
libexec/trinity/util/support_scripts/SAM_to_frag_coords.pl
libexec/trinity/util/support_scripts/scaffold_iworm_contigs.pl
libexec/trinity/util/support_scripts/segment_GFF_partitions.pl
libexec/trinity/util/support_scripts/wig_clip_to_bed.pl
libexec/trinity/util/TrinityStats.pl
