%FILES%
usr/
usr/bin/
usr/bin/BubbleUpClustering
usr/bin/Chrysalis
usr/bin/CreateIwormFastaBundle
usr/bin/FastaToDeBruijn
usr/bin/GraphFromFasta
usr/bin/QuantifyGraph
usr/bin/ReadsToTranscripts
usr/bin/Trinity
usr/bin/fastaToKmerCoverageStats
usr/bin/inchworm
usr/bin/seqtk-trinity
usr/share/
usr/share/java/
usr/share/java/Butterfly.jar
usr/share/trinityrnaseq/
usr/share/trinityrnaseq/Analysis/
usr/share/trinityrnaseq/Analysis/Compact_graph_partial.py
usr/share/trinityrnaseq/Analysis/Compact_graph_pruner.py
usr/share/trinityrnaseq/Analysis/Compact_graph_whole.py
usr/share/trinityrnaseq/Analysis/DE_graph_to_dot.pl
usr/share/trinityrnaseq/Analysis/DE_pair_counts_to_matrix.pl
usr/share/trinityrnaseq/Analysis/DE_results_to_pairwise_summary.pl
usr/share/trinityrnaseq/Analysis/DP_matrix.py
usr/share/trinityrnaseq/Analysis/DTE_to_DTU.pl
usr/share/trinityrnaseq/Analysis/EBSeq_to_pairwise_summary.pl
usr/share/trinityrnaseq/Analysis/FL_trans_analysis_pipeline.pl
usr/share/trinityrnaseq/Analysis/GOplot.Rscript
usr/share/trinityrnaseq/Analysis/Gene_splice_modeler.py
usr/share/trinityrnaseq/Analysis/Glimma.Trinity.Rscript
usr/share/trinityrnaseq/Analysis/GraphCycleException.py
usr/share/trinityrnaseq/Analysis/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
usr/share/trinityrnaseq/Analysis/Node_alignment.py
usr/share/trinityrnaseq/Analysis/Node_path.py
usr/share/trinityrnaseq/Analysis/PtR
usr/share/trinityrnaseq/Analysis/README.md
usr/share/trinityrnaseq/Analysis/ROKU.pl
usr/share/trinityrnaseq/Analysis/Splice_model_refiner.py
usr/share/trinityrnaseq/Analysis/TGLOBALS.py
usr/share/trinityrnaseq/Analysis/TGraph.py
usr/share/trinityrnaseq/Analysis/TNode.py
usr/share/trinityrnaseq/Analysis/Topological_sort.py
usr/share/trinityrnaseq/Analysis/Trinity_fasta_parser.py
usr/share/trinityrnaseq/Analysis/Trinity_gene_splice_modeler.py
usr/share/trinityrnaseq/Analysis/Trinity_util.py
usr/share/trinityrnaseq/Analysis/VCF_to_annotated_SNP_report.pl
usr/share/trinityrnaseq/Analysis/__init__.py
usr/share/trinityrnaseq/Analysis/add_annot_to_trans_id.pl
usr/share/trinityrnaseq/Analysis/add_annotations_to_GO_and_lengths_file.R
usr/share/trinityrnaseq/Analysis/add_blastx_hit_to_trinity_id.pl
usr/share/trinityrnaseq/Analysis/add_counts_to_classes.pl
usr/share/trinityrnaseq/Analysis/aln_before_after.pl
usr/share/trinityrnaseq/Analysis/analyze_diff_expr.pl
usr/share/trinityrnaseq/Analysis/assign_tissue_specific.pl
usr/share/trinityrnaseq/Analysis/blat_full_length_mappings.pl
usr/share/trinityrnaseq/Analysis/blat_map_filter_with_isoforms.pl
usr/share/trinityrnaseq/Analysis/blat_psl_to_align_summary_stats.pl
usr/share/trinityrnaseq/Analysis/blat_query_top_hit_extractor.pl
usr/share/trinityrnaseq/Analysis/blat_top_tier_genes.pl
usr/share/trinityrnaseq/Analysis/boot.tree.R
usr/share/trinityrnaseq/Analysis/class_to_separate_fpkm_matrices.pl
usr/share/trinityrnaseq/Analysis/clean_bam.pl
usr/share/trinityrnaseq/Analysis/cleanme.pl
usr/share/trinityrnaseq/Analysis/compare_gene_trans_DE_ranks.pl
usr/share/trinityrnaseq/Analysis/compute_oracle.pl
usr/share/trinityrnaseq/Analysis/count_by_expression_quintile.pl
usr/share/trinityrnaseq/Analysis/cut_tree_into_clusters.pl
usr/share/trinityrnaseq/Analysis/define_clusters_by_cutting_tree.pl
usr/share/trinityrnaseq/Analysis/dexseq_wrapper.pl
usr/share/trinityrnaseq/Analysis/diff_expr_analysis_to_heatmap_html.pl
usr/share/trinityrnaseq/Analysis/diff_express.cgi
usr/share/trinityrnaseq/Analysis/downsample_count_matrix.pl
usr/share/trinityrnaseq/Analysis/edgeR.TMM.minimal.R
usr/share/trinityrnaseq/Analysis/edgeR_funcs.R
usr/share/trinityrnaseq/Analysis/edgeR_to_pairwise_summary.pl
usr/share/trinityrnaseq/Analysis/es.mef.fpkm.matrix
usr/share/trinityrnaseq/Analysis/examine_rank_correlation.pl
usr/share/trinityrnaseq/Analysis/extract_GO_enriched_genes.pl
usr/share/trinityrnaseq/Analysis/extract_supertranscript_from_reference.py
usr/share/trinityrnaseq/Analysis/extract_venn_agree_from_summaries.pl
usr/share/trinityrnaseq/Analysis/filter_diff_expr.pl
usr/share/trinityrnaseq/Analysis/filter_matrix_min_sum_rowcounts.pl
usr/share/trinityrnaseq/Analysis/fusion_comparisons_via_maps_files.pl
usr/share/trinityrnaseq/Analysis/get_cluster_info.R
usr/share/trinityrnaseq/Analysis/get_genes_from_maps_file.pl
usr/share/trinityrnaseq/Analysis/get_tissue_enriched_DE_one_vs_all.pl
usr/share/trinityrnaseq/Analysis/get_transcript_lengths.pl
usr/share/trinityrnaseq/Analysis/group_isoforms_by_tissue_enrichment.pl
usr/share/trinityrnaseq/Analysis/heatmap.3.R
usr/share/trinityrnaseq/Analysis/identify_diff_isoform_splicing.pl
usr/share/trinityrnaseq/Analysis/jaccard_distance.R
usr/share/trinityrnaseq/Analysis/log2_transform_matrix.pl
usr/share/trinityrnaseq/Analysis/log2_transform_median_center_fpkm_matrix.pl
usr/share/trinityrnaseq/Analysis/manually_define_clusters.R
usr/share/trinityrnaseq/Analysis/maps_file_to_paralog_representation.pl
usr/share/trinityrnaseq/Analysis/matrix_to_gene_plots.pl
usr/share/trinityrnaseq/Analysis/merge_matrices.pl
usr/share/trinityrnaseq/Analysis/merge_subclusters.pl
usr/share/trinityrnaseq/Analysis/misc_rnaseq_funcs.R
usr/share/trinityrnaseq/Analysis/mmdiff_to_pairwise_summary.pl
usr/share/trinityrnaseq/Analysis/notes
usr/share/trinityrnaseq/Analysis/oracle_counter.pl
usr/share/trinityrnaseq/Analysis/orig.samples.txt
usr/share/trinityrnaseq/Analysis/pairs3.R
usr/share/trinityrnaseq/Analysis/pairwise_DE_summary_to_DE_classification.pl
usr/share/trinityrnaseq/Analysis/plot_all_DE_MAplots.Rscript
usr/share/trinityrnaseq/Analysis/plot_all_DE_volcanos.Rscript
usr/share/trinityrnaseq/Analysis/plot_expression_patterns.pl
usr/share/trinityrnaseq/Analysis/plot_log2FC_hist.Rscript
usr/share/trinityrnaseq/Analysis/prep_n_run_GOplot.pl
usr/share/trinityrnaseq/Analysis/prune_isoforms_fasta.pl
usr/share/trinityrnaseq/Analysis/prune_isoforms_gtf.pl
usr/share/trinityrnaseq/Analysis/rank_roku_by_expr.pl
usr/share/trinityrnaseq/Analysis/reformat_featureCounts.pl
usr/share/trinityrnaseq/Analysis/remove_batch_effects_from_count_matrix.pl
usr/share/trinityrnaseq/Analysis/rename_matrix_column_labels.pl
usr/share/trinityrnaseq/Analysis/rename_matrix_feature_identifiers.pl
usr/share/trinityrnaseq/Analysis/replicates_to_sample_averages_matrix.pl
usr/share/trinityrnaseq/Analysis/rnaseq_plot_funcs.R
usr/share/trinityrnaseq/Analysis/runMe.sh
usr/share/trinityrnaseq/Analysis/run_DE_analysis.pl
usr/share/trinityrnaseq/Analysis/run_GOseq.pl
usr/share/trinityrnaseq/Analysis/run_TMM_normalization_write_FPKM_matrix.pl
usr/share/trinityrnaseq/Analysis/run_variant_calling.py
usr/share/trinityrnaseq/Analysis/samples.txt
usr/share/trinityrnaseq/Analysis/stratify_diff_expression.pl
usr/share/trinityrnaseq/Analysis/subcluster_to_canvasXpress_html.make_index_html.pl
usr/share/trinityrnaseq/Analysis/subcluster_to_canvasXpress_html.pl
usr/share/trinityrnaseq/Analysis/summarize_diff_expr_across_min_threshold_ranges.pl
usr/share/trinityrnaseq/Analysis/test.heatmap.3.R
usr/share/trinityrnaseq/Analysis/test.html
usr/share/trinityrnaseq/Analysis/test_heatmap_w_pca.R
usr/share/trinityrnaseq/Analysis/test_session.html
usr/share/trinityrnaseq/Analysis/tier_gene_trans_alignments.pl
usr/share/trinityrnaseq/Analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl
usr/share/trinityrnaseq/Analysis/trinity_to_genomeview_html.pl
usr/share/trinityrnaseq/Analysis/validate_UP_subset.Rscript
usr/share/trinityrnaseq/Analysis/venn_pairwise_summaries.pair_stats.pl
usr/share/trinityrnaseq/Analysis/venn_pairwise_summaries.pl
usr/share/trinityrnaseq/Analysis/vioplot2.R
usr/share/trinityrnaseq/PerlLib/
usr/share/trinityrnaseq/PerlLib/AlignGraph.pm
usr/share/trinityrnaseq/PerlLib/AlignNode.pm
usr/share/trinityrnaseq/PerlLib/Alignment_segment.pm
usr/share/trinityrnaseq/PerlLib/Alternative_splice_comparer.pm
usr/share/trinityrnaseq/PerlLib/Ascii_genome_illustrator.pm
usr/share/trinityrnaseq/PerlLib/BED_utils.pm
usr/share/trinityrnaseq/PerlLib/BHStats.pm
usr/share/trinityrnaseq/PerlLib/CDNA_alignment.pm
usr/share/trinityrnaseq/PerlLib/CDNA_stitcher.pm
usr/share/trinityrnaseq/PerlLib/CIGAR.pm
usr/share/trinityrnaseq/PerlLib/CMD_processor.pm
usr/share/trinityrnaseq/PerlLib/COMMON.pm
usr/share/trinityrnaseq/PerlLib/ColorGradient.pm
usr/share/trinityrnaseq/PerlLib/DelimParser.pm
usr/share/trinityrnaseq/PerlLib/EM.pm
usr/share/trinityrnaseq/PerlLib/Exons_to_geneobj.pm
usr/share/trinityrnaseq/PerlLib/Fasta_reader.pm
usr/share/trinityrnaseq/PerlLib/Fasta_retriever.pm
usr/share/trinityrnaseq/PerlLib/Fastq_reader.pm
usr/share/trinityrnaseq/PerlLib/GFF3_alignment_utils.pm
usr/share/trinityrnaseq/PerlLib/GFF3_utils.pm
usr/share/trinityrnaseq/PerlLib/GFF_maker.pm
usr/share/trinityrnaseq/PerlLib/GTF.pm
usr/share/trinityrnaseq/PerlLib/GTF_utils.pm
usr/share/trinityrnaseq/PerlLib/Gene_obj.pm
usr/share/trinityrnaseq/PerlLib/Gene_obj_alignment_assembler.pm
usr/share/trinityrnaseq/PerlLib/Gene_obj_indexer.pm
usr/share/trinityrnaseq/PerlLib/GenericGraph.pm
usr/share/trinityrnaseq/PerlLib/GenericNode.pm
usr/share/trinityrnaseq/PerlLib/Genome_based_cDNA_assembler.pm
usr/share/trinityrnaseq/PerlLib/Genome_based_cDNA_graph_assembler.pm
usr/share/trinityrnaseq/PerlLib/Heatmap.pm
usr/share/trinityrnaseq/PerlLib/KmerGraph.pm
usr/share/trinityrnaseq/PerlLib/KmerNode.pm
usr/share/trinityrnaseq/PerlLib/Ktree.pm
usr/share/trinityrnaseq/PerlLib/Longest_orf.pm
usr/share/trinityrnaseq/PerlLib/Nuc_translator.pm
usr/share/trinityrnaseq/PerlLib/Overlap_assembler.pm
usr/share/trinityrnaseq/PerlLib/Overlap_info.pm
usr/share/trinityrnaseq/PerlLib/Overlap_piler.pm
usr/share/trinityrnaseq/PerlLib/PASA_alignment_assembler.pm
usr/share/trinityrnaseq/PerlLib/PSL_parser.pm
usr/share/trinityrnaseq/PerlLib/Pipeliner.pm
usr/share/trinityrnaseq/PerlLib/Process_cmd.pm
usr/share/trinityrnaseq/PerlLib/ReadCoverageGraph.pm
usr/share/trinityrnaseq/PerlLib/ReadCoverageNode.pm
usr/share/trinityrnaseq/PerlLib/ReadManager.pm
usr/share/trinityrnaseq/PerlLib/ReadTracker.pm
usr/share/trinityrnaseq/PerlLib/SAM_entry.pm
usr/share/trinityrnaseq/PerlLib/SAM_reader.pm
usr/share/trinityrnaseq/PerlLib/SAM_to_AlignGraph.pm
usr/share/trinityrnaseq/PerlLib/SingleLinkageClusterer.pm
usr/share/trinityrnaseq/PerlLib/Splice_graph_assembler.pm
usr/share/trinityrnaseq/PerlLib/StringGraph.pm
usr/share/trinityrnaseq/PerlLib/StringNode.pm
usr/share/trinityrnaseq/PerlLib/Thread_helper.pm
usr/share/trinityrnaseq/PerlLib/TiedHash.pm
usr/share/trinityrnaseq/PerlLib/Uniform_Read_Generator.pm
usr/share/trinityrnaseq/PerlLib/VCF_parser.pm
usr/share/trinityrnaseq/PerlLib/WigParser.pm
usr/share/trinityrnaseq/PerlLib/overlapping_nucs.ph
usr/share/trinityrnaseq/PerlLib/test_Fasta_retriever.pl
usr/share/trinityrnaseq/PerlLib/test_htc_gridrunner_LSF.pl
usr/share/trinityrnaseq/PerlLib/test_htc_gridrunner_SGE.pl
usr/share/trinityrnaseq/PyLib/
usr/share/trinityrnaseq/PyLib/Pipeliner.py
usr/share/trinityrnaseq/Trinity
usr/share/trinityrnaseq/trinity-plugins/
usr/share/trinityrnaseq/trinity-plugins/COLLECTL/
usr/share/trinityrnaseq/trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
usr/share/trinityrnaseq/trinity-plugins/COLLECTL/util/
usr/share/trinityrnaseq/trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py
usr/share/trinityrnaseq/trinity-plugins/COLLECTL/util/plot_time_vs_resource.Rscript
usr/share/trinityrnaseq/trinity-plugins/DEXseq_util/
usr/share/trinityrnaseq/trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
usr/share/trinityrnaseq/trinity-plugins/bamsifter/
usr/share/trinityrnaseq/trinity-plugins/bamsifter/bamsifter
usr/share/trinityrnaseq/util/
usr/share/trinityrnaseq/util/ButterflyFastaToGraphDot.pl
usr/share/trinityrnaseq/util/ExitTester.jar
usr/share/trinityrnaseq/util/GG_partitioned_trinity_aggregator.pl
usr/share/trinityrnaseq/util/HiCpipe_nameSortedSam_to_raw.pl
usr/share/trinityrnaseq/util/Monarch
usr/share/trinityrnaseq/util/N50.pl
usr/share/trinityrnaseq/util/N50stats.pl
usr/share/trinityrnaseq/util/README
usr/share/trinityrnaseq/util/SAM_coordSorted_fragment_Read_coverage_writer.pl
usr/share/trinityrnaseq/util/SAM_coordSorted_fragment_coverage_writer2.pl
usr/share/trinityrnaseq/util/SAM_coordsorted_max_reads_per_position.pl
usr/share/trinityrnaseq/util/SAM_extract_properly_mapped_pairs.pl
usr/share/trinityrnaseq/util/SAM_extract_uniquely_mapped_reads.pl
usr/share/trinityrnaseq/util/SAM_filter_out_unmapped_reads.pl
usr/share/trinityrnaseq/util/SAM_intron_extractor.pl
usr/share/trinityrnaseq/util/SAM_nameSorted_to_uniq_count_stats.pl
usr/share/trinityrnaseq/util/SAM_ordered_pair_jaccard.pl
usr/share/trinityrnaseq/util/SAM_pair_to_bed.pl
usr/share/trinityrnaseq/util/SAM_set_transcribed_orient_info.pl
usr/share/trinityrnaseq/util/SAM_show_alignment.pl
usr/share/trinityrnaseq/util/SAM_show_alignment.summarize_stats.pl
usr/share/trinityrnaseq/util/SAM_sortAny_to_count_stats.pl
usr/share/trinityrnaseq/util/SAM_strand_separator.pl
usr/share/trinityrnaseq/util/SAM_toString.pl
usr/share/trinityrnaseq/util/SAM_to_bed.pl
usr/share/trinityrnaseq/util/SAM_to_fasta.pl
usr/share/trinityrnaseq/util/SAM_to_frag_coords.pl
usr/share/trinityrnaseq/util/SAM_to_gff3.minimap2.pl
usr/share/trinityrnaseq/util/SRA_to_fastq.notes
usr/share/trinityrnaseq/util/SRA_to_fastq.pl
usr/share/trinityrnaseq/util/STAR_align_log_parser.py
usr/share/trinityrnaseq/util/SegmentGraph.pm
usr/share/trinityrnaseq/util/TPM_weighted_gene_length.py
usr/share/trinityrnaseq/util/TRINITY.CONFIG.template
usr/share/trinityrnaseq/util/TophatCufflinksWrapper.pl
usr/share/trinityrnaseq/util/TrinityStats.pl
usr/share/trinityrnaseq/util/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
usr/share/trinityrnaseq/util/Trinity_node_seq_extractor.pl
usr/share/trinityrnaseq/util/abundance_estimates_to_matrix.pl
usr/share/trinityrnaseq/util/acc_list_to_fasta_entries.pl
usr/share/trinityrnaseq/util/add_LR_reads_to_iworm_bundle.pl
usr/share/trinityrnaseq/util/alexie_analyze_blast.pl
usr/share/trinityrnaseq/util/align_and_estimate_abundance.pl
usr/share/trinityrnaseq/util/align_reads_launch_igv.pl
usr/share/trinityrnaseq/util/allele_simulator.pl
usr/share/trinityrnaseq/util/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
usr/share/trinityrnaseq/util/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
usr/share/trinityrnaseq/util/analyze_blastPlus_topHit_coverage.extract_OS.pl
usr/share/trinityrnaseq/util/analyze_blastPlus_topHit_coverage.org_matrix.pl
usr/share/trinityrnaseq/util/analyze_blastPlus_topHit_coverage.pl
usr/share/trinityrnaseq/util/annotate_chrysalis_welds_with_iworm_names.pl
usr/share/trinityrnaseq/util/assess_intron_path_sensitivity.pl
usr/share/trinityrnaseq/util/assess_intron_path_sensitivity.summarizer.pl
usr/share/trinityrnaseq/util/audit_summary_stats.pl
usr/share/trinityrnaseq/util/audit_summary_stats.reexamine.pl
usr/share/trinityrnaseq/util/average.pl
usr/share/trinityrnaseq/util/bam_to_cuff.pl
usr/share/trinityrnaseq/util/batch_cmds.pl
usr/share/trinityrnaseq/util/blast_outfmt6_group_segments.pl
usr/share/trinityrnaseq/util/blast_outfmt6_group_segments.to_Markov_Clustering.pl
usr/share/trinityrnaseq/util/blast_outfmt6_group_segments.tophit_coverage.pl
usr/share/trinityrnaseq/util/blastn_wrapper.pl
usr/share/trinityrnaseq/util/blat_sam_add_reads2.pl
usr/share/trinityrnaseq/util/blat_to_sam.pl
usr/share/trinityrnaseq/util/blat_top_hit_extractor.pl
usr/share/trinityrnaseq/util/bowtie2_wrapper.pl
usr/share/trinityrnaseq/util/capture_orig_n_unmapped_reads.pl
usr/share/trinityrnaseq/util/cat_require_newlines.pl
usr/share/trinityrnaseq/util/cdhit_examine_isoforms.pl
usr/share/trinityrnaseq/util/cdna_fasta_file_to_transcript_gtf.pl
usr/share/trinityrnaseq/util/check_chrysalis_graph_reciprocal_edges.pl
usr/share/trinityrnaseq/util/check_fastQ_pair_ordering.pl
usr/share/trinityrnaseq/util/chrys_graph_to_dot.pl
usr/share/trinityrnaseq/util/collate_fqs.pl
usr/share/trinityrnaseq/util/combined_nameSorted_to_dup_pairs_removed.pl
usr/share/trinityrnaseq/util/compare_FL_stats.pl
usr/share/trinityrnaseq/util/compare_bflies.pl
usr/share/trinityrnaseq/util/component_to_graph_dot.pl
usr/share/trinityrnaseq/util/contig_ExN50_statistic.pl
usr/share/trinityrnaseq/util/convert_fasta_identifiers_for_FL_analysis.pl
usr/share/trinityrnaseq/util/count_N50_given_MIN_FPKM_threshold.pl
usr/share/trinityrnaseq/util/count_features_given_MIN_FPKM_threshold.pl
usr/share/trinityrnaseq/util/count_iso_per_gene_dist.pl
usr/share/trinityrnaseq/util/count_matrix_features_given_MIN_TPM_threshold.pl
usr/share/trinityrnaseq/util/count_number_fasta_seqs.pl
usr/share/trinityrnaseq/util/count_trans_per_component.pl
usr/share/trinityrnaseq/util/cuff_gtf_to_bed.pl
usr/share/trinityrnaseq/util/decode_SAM_flag_value.pl
usr/share/trinityrnaseq/util/define_SAM_coverage_partitions2.pl
usr/share/trinityrnaseq/util/define_coverage_partitions.pl
usr/share/trinityrnaseq/util/describe_SAM_read_flag_info.pl
usr/share/trinityrnaseq/util/determine_RF_strand_specificity.pl
usr/share/trinityrnaseq/util/diff_splice_paths.pl
usr/share/trinityrnaseq/util/eXpress_trans_to_gene_results.pl
usr/share/trinityrnaseq/util/ensure_coord_sorted_sam.pl
usr/share/trinityrnaseq/util/ensure_paired_end_bam_file.pl
usr/share/trinityrnaseq/util/examine_iworm_FL_across_threads.pl
usr/share/trinityrnaseq/util/examine_strand_specificity.pl
usr/share/trinityrnaseq/util/examine_weldmer_halves.pl
usr/share/trinityrnaseq/util/expression_analysis_lib.R
usr/share/trinityrnaseq/util/extract_bam_reads_per_target_gene.pl
usr/share/trinityrnaseq/util/extract_bam_reads_per_target_transcript.pl
usr/share/trinityrnaseq/util/extract_fastQ_pairings.pl
usr/share/trinityrnaseq/util/extract_reads_per_partition.pl
usr/share/trinityrnaseq/util/fan_out_fasta_seqs_to_indiv_files.pl
usr/share/trinityrnaseq/util/fastQ_append_acc.pl
usr/share/trinityrnaseq/util/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
usr/share/trinityrnaseq/util/fastQ_rand_subset.pl
usr/share/trinityrnaseq/util/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
usr/share/trinityrnaseq/util/fastQ_to_fastA.pl
usr/share/trinityrnaseq/util/fastQ_to_tab.pl
usr/share/trinityrnaseq/util/fastQ_top_N_records.pl
usr/share/trinityrnaseq/util/fasta_file_reformatter.pl
usr/share/trinityrnaseq/util/fasta_filter_by_min_length.pl
usr/share/trinityrnaseq/util/fasta_find_duplicates.pl
usr/share/trinityrnaseq/util/fasta_remove_duplicates.pl
usr/share/trinityrnaseq/util/fasta_seq_length.pl
usr/share/trinityrnaseq/util/fasta_to_cmd_generator.pl
usr/share/trinityrnaseq/util/fasta_to_tab.pl
usr/share/trinityrnaseq/util/fasta_write_sense_n_anti.pl
usr/share/trinityrnaseq/util/fastq_cleaner.pl
usr/share/trinityrnaseq/util/fastq_interleave_pairs.pl
usr/share/trinityrnaseq/util/fastq_merge_sorted_tab_lists.pl
usr/share/trinityrnaseq/util/fastq_stats.pl
usr/share/trinityrnaseq/util/fastq_unweave_pairs.pl
usr/share/trinityrnaseq/util/filter_iworm_by_min_length_or_cov.pl
usr/share/trinityrnaseq/util/filter_low_expr_transcripts.pl
usr/share/trinityrnaseq/util/filter_out_accs_from_fasta.pl
usr/share/trinityrnaseq/util/filter_similar_seqs_expr_and_strand_aware.pl
usr/share/trinityrnaseq/util/filter_transcripts_require_min_cov.pl
usr/share/trinityrnaseq/util/find_pruned_edges_shouldve_kept.pl
usr/share/trinityrnaseq/util/flattened_gff_n_genome_to_Trinity_emulator.pl
usr/share/trinityrnaseq/util/frag_boundary_to_wig.pl
usr/share/trinityrnaseq/util/frag_to_bed.pl
usr/share/trinityrnaseq/util/fragment_coverage_writer.pl
usr/share/trinityrnaseq/util/gene_gff3_to_bed_cmds.pl
usr/share/trinityrnaseq/util/gene_gff3_to_introns.pl
usr/share/trinityrnaseq/util/gene_to_shared_transcript_content.pl
usr/share/trinityrnaseq/util/generate_gene_alt_splicing_graphs.pl
usr/share/trinityrnaseq/util/generate_trans_graphs.pl
usr/share/trinityrnaseq/util/genome_gff3_to_gene_gff3_partitions.pl
usr/share/trinityrnaseq/util/genwig.sh
usr/share/trinityrnaseq/util/genwig2.py
usr/share/trinityrnaseq/util/get_GC_content_dist.pl
usr/share/trinityrnaseq/util/get_Poisson_conf_intervals.R
usr/share/trinityrnaseq/util/get_Trinity_gene_to_trans_map.pl
usr/share/trinityrnaseq/util/get_longest_isoform_seq_per_trinity_gene.pl
usr/share/trinityrnaseq/util/get_path_nodes_from_fasta.pl
usr/share/trinityrnaseq/util/get_welds_from_chrysals_graphFromFasta_out.pl
usr/share/trinityrnaseq/util/gff3_file_to_cdna.pl
usr/share/trinityrnaseq/util/gff3_file_utr_coverage_trimmer.pl
usr/share/trinityrnaseq/util/gff3_to_genome_feature_base_encoding.parse_SAM.pl
usr/share/trinityrnaseq/util/gff3_to_genome_feature_base_encoding.pl
usr/share/trinityrnaseq/util/gmap_gff3_chimera_jaccard_analyzer.pl
usr/share/trinityrnaseq/util/gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
usr/share/trinityrnaseq/util/gmap_gff3_to_percent_length_stats.pl
usr/share/trinityrnaseq/util/gmap_native_to_format_converter.pl
usr/share/trinityrnaseq/util/gmap_to_ref.pl
usr/share/trinityrnaseq/util/graph_out_to_bfly_cmd.pl
usr/share/trinityrnaseq/util/gtf_to_bed_format.pl
usr/share/trinityrnaseq/util/gtf_to_introns.pl
usr/share/trinityrnaseq/util/harvest_transcripts.pl
usr/share/trinityrnaseq/util/hicpipe_raw_converter.pl
usr/share/trinityrnaseq/util/identify_distal_isoform_variations.pl
usr/share/trinityrnaseq/util/illustrate_ref_comparison.pl
usr/share/trinityrnaseq/util/inchworm_transcript_splitter.pl
usr/share/trinityrnaseq/util/info_files_to_eval_cmds.pl
usr/share/trinityrnaseq/util/insilico_read_normalization.pl
usr/share/trinityrnaseq/util/intron_barcharter.pl
usr/share/trinityrnaseq/util/iworm_LR_to_scaff_pairs.pl
usr/share/trinityrnaseq/util/iworm_welds_to_dot.pl
usr/share/trinityrnaseq/util/jaccard_fasta_clipper.pl
usr/share/trinityrnaseq/util/jaccard_sam_pair_refiner.pl
usr/share/trinityrnaseq/util/jaccard_wig_clipper.pl
usr/share/trinityrnaseq/util/join_any.pl
usr/share/trinityrnaseq/util/join_by_left_col.pl
usr/share/trinityrnaseq/util/join_expr_vals_single_table.pl
usr/share/trinityrnaseq/util/join_multi_wig_to_graph_plot.pl
usr/share/trinityrnaseq/util/join_partitions_within_range.pl
usr/share/trinityrnaseq/util/kallisto_trans_to_gene_results.pl
usr/share/trinityrnaseq/util/kmer_counter.pl
usr/share/trinityrnaseq/util/kmer_histo.NormMaxKCov50.txt
usr/share/trinityrnaseq/util/kmer_histo.all.txt
usr/share/trinityrnaseq/util/m8_blastclust.pl
usr/share/trinityrnaseq/util/map_gtf_transcripts_to_genome_annots.pl
usr/share/trinityrnaseq/util/merge_RSEM_output_to_matrix.pl
usr/share/trinityrnaseq/util/merge_blast_n_rsem_results.pl
usr/share/trinityrnaseq/util/merge_pair_and_LR_scaff_links.pl
usr/share/trinityrnaseq/util/merge_replicate_bams_via_samples_file.pl
usr/share/trinityrnaseq/util/merge_rsem_n_express_for_compare.pl
usr/share/trinityrnaseq/util/mpi_iworm_proc_contigs_to_fa.pl
usr/share/trinityrnaseq/util/nameSorted_SAM_to_FastQ.pl
usr/share/trinityrnaseq/util/nameSorted_SAM_to_paired_fastq.pl
usr/share/trinityrnaseq/util/nbkc_merge_left_right_stats.pl
usr/share/trinityrnaseq/util/nbkc_normalize.pl
usr/share/trinityrnaseq/util/notes
usr/share/trinityrnaseq/util/omp_iworm_thread_contigs_to_fa.pl
usr/share/trinityrnaseq/util/ordered_fragment_coords_to_jaccard.pl
usr/share/trinityrnaseq/util/organize_data_table_by_trinity_component.pl
usr/share/trinityrnaseq/util/outfmt6_add_percent_match_length.pl
usr/share/trinityrnaseq/util/pair_up_fastq_files_1_2.pl
usr/share/trinityrnaseq/util/pair_up_fastq_files_LeftRight.pl
usr/share/trinityrnaseq/util/pair_up_fastq_files_R1_R2.pl
usr/share/trinityrnaseq/util/pairwise_kmer_content_comparer.pl
usr/share/trinityrnaseq/util/partition_chrysalis_graphs_n_reads.pl
usr/share/trinityrnaseq/util/partition_target_transcripts.pl
usr/share/trinityrnaseq/util/partitioned_trinity_aggregator.pl
usr/share/trinityrnaseq/util/pbs_check.pl
usr/share/trinityrnaseq/util/plot_ExN50_statistic.Rscript
usr/share/trinityrnaseq/util/plot_expressed_gene_dist.pl
usr/share/trinityrnaseq/util/plot_me.R
usr/share/trinityrnaseq/util/plot_strand_specificity_dist_by_quantile.Rscript
usr/share/trinityrnaseq/util/plugin_install_tests.sh
usr/share/trinityrnaseq/util/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
usr/share/trinityrnaseq/util/print.pl
usr/share/trinityrnaseq/util/print_butterfly_assemblies.pl
usr/share/trinityrnaseq/util/print_kmers.pl
usr/share/trinityrnaseq/util/process_BLAT_alignments.pl
usr/share/trinityrnaseq/util/process_GMAP_alignments_gff3_chimeras_ok.pl
usr/share/trinityrnaseq/util/process_minimap2_alignments.pl
usr/share/trinityrnaseq/util/prop_pair_sam_refiner.pl
usr/share/trinityrnaseq/util/pslx_to_gff3.pl
usr/share/trinityrnaseq/util/randomly_mutate_seqs.pl
usr/share/trinityrnaseq/util/randomly_sample_PE_fastq.pl
usr/share/trinityrnaseq/util/remove_cntrl_chars.pl
usr/share/trinityrnaseq/util/rename_fasta_accessions_using_Trinotate_annot_mappings.pl
usr/share/trinityrnaseq/util/result.pdf
usr/share/trinityrnaseq/util/retrieve_sequences_from_fasta.pl
usr/share/trinityrnaseq/util/revcomp_fasta.pl
usr/share/trinityrnaseq/util/row_to_column.pl
usr/share/trinityrnaseq/util/run_BLAT_shortReads.pl
usr/share/trinityrnaseq/util/run_DETONATE.pl
usr/share/trinityrnaseq/util/run_GSNAP.pl
usr/share/trinityrnaseq/util/run_HISAT.pl
usr/share/trinityrnaseq/util/run_HISAT2_via_samples_file.pl
usr/share/trinityrnaseq/util/run_HiCpipe_bowtie.pl
usr/share/trinityrnaseq/util/run_STAR.pl
usr/share/trinityrnaseq/util/run_STAR_via_samples_file.pl
usr/share/trinityrnaseq/util/run_Stringtie_via_bam_file_list.pl
usr/share/trinityrnaseq/util/run_TMM_scale_matrix.pl
usr/share/trinityrnaseq/util/run_TOPHAT.pl
usr/share/trinityrnaseq/util/run_Trinity_eval.pl
usr/share/trinityrnaseq/util/run_Trinity_eval.sh
usr/share/trinityrnaseq/util/run_UpperQuartileNormalization_matrix.pl
usr/share/trinityrnaseq/util/run_bowtie2.pl
usr/share/trinityrnaseq/util/run_bwa.pl
usr/share/trinityrnaseq/util/run_bwasw_trinity.pl
usr/share/trinityrnaseq/util/run_jellyfish.pl
usr/share/trinityrnaseq/util/run_read_simulator_per_fasta_entry.pl
usr/share/trinityrnaseq/util/run_read_simulator_per_gene.pl
usr/share/trinityrnaseq/util/run_simulate_reads.wgsim.pl
usr/share/trinityrnaseq/util/run_trimmomatic_qual_trimming.pl
usr/share/trinityrnaseq/util/run_trinity_WITH_LR.pl
usr/share/trinityrnaseq/util/run_trinity_no_LR.pl
usr/share/trinityrnaseq/util/salmon_runner.pl
usr/share/trinityrnaseq/util/salmon_trans_to_gene_results.pl
usr/share/trinityrnaseq/util/sample_data_tests.py
usr/share/trinityrnaseq/util/scaffold_iworm_contigs.pl
usr/share/trinityrnaseq/util/segment_GFF_partitions.pl
usr/share/trinityrnaseq/util/seqinfo_refseq_to_dot.pl
usr/share/trinityrnaseq/util/shuffle.pl
usr/share/trinityrnaseq/util/sift_bam_max_cov.pl
usr/share/trinityrnaseq/util/sim_reads.pl
usr/share/trinityrnaseq/util/sim_single_bubble.pl
usr/share/trinityrnaseq/util/simulate_illuminaPE_from_transcripts.pl
usr/share/trinityrnaseq/util/simulate_illuminaPE_from_transcripts.wgsim.pl
usr/share/trinityrnaseq/util/simulate_reads_sam_and_fa.pl
usr/share/trinityrnaseq/util/sixFrameTranslation.pl
usr/share/trinityrnaseq/util/sort_fastq.pl
usr/share/trinityrnaseq/util/strip_fasta_header.pl
usr/share/trinityrnaseq/util/tab_to_fastQ.pl
usr/share/trinityrnaseq/util/tab_to_fasta.pl
usr/share/trinityrnaseq/util/tblastn_wrapper.pl
usr/share/trinityrnaseq/util/testUnlimitStacksize.pl
usr/share/trinityrnaseq/util/test_prep.py
usr/share/trinityrnaseq/util/tests.py
usr/share/trinityrnaseq/util/top_blat_sam_extractor.pl
usr/share/trinityrnaseq/util/trans_gff3_to_bed_cmds.pl
usr/share/trinityrnaseq/util/transcript_coverage_UTR_trimmer.pl
usr/share/trinityrnaseq/util/transcript_fasta_to_ORF_pics.pl
usr/share/trinityrnaseq/util/transcript_gff3_to_bed.pl
usr/share/trinityrnaseq/util/transdecoder_pep_to_false_fusion_finder.pl
usr/share/trinityrnaseq/util/trinity_component_distribution.pl
usr/share/trinityrnaseq/util/trinity_install_tests.sh
usr/share/trinityrnaseq/util/trinity_installer.py
usr/share/trinityrnaseq/util/trinity_kill.pl
usr/share/trinityrnaseq/util/trinity_kill.sh
usr/share/trinityrnaseq/util/trinity_pbs.cont
usr/share/trinityrnaseq/util/trinity_pbs.header
usr/share/trinityrnaseq/util/trinity_pbs.p1
usr/share/trinityrnaseq/util/trinity_pbs.p2
usr/share/trinityrnaseq/util/trinity_pbs.p3
usr/share/trinityrnaseq/util/trinity_pbs.p4a
usr/share/trinityrnaseq/util/trinity_pbs.p4b
usr/share/trinityrnaseq/util/trinity_pbs.p5b
usr/share/trinityrnaseq/util/trinity_pbs.sh
usr/share/trinityrnaseq/util/trinity_trans_matrix_to_rep_trans_gene_matrix.pl
usr/share/trinityrnaseq/util/try_estimate_TPM_filtering_threshold.Rscript
usr/share/trinityrnaseq/util/validate_fastqs.py
usr/share/trinityrnaseq/util/wig_clip_to_bed.pl
usr/share/trinityrnaseq/util/write_partitioned_trinity_cmds.pl
usr/share/trinityrnaseq/util/write_simulate_read_commands.pl
usr/share/trinityrnaseq/util/write_trin_cmds.pl
