616 lines
39 KiB
Plaintext
616 lines
39 KiB
Plaintext
@comment $NetBSD$
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bin/Trinity
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libexec/trinity/Analysis/DifferentialExpression/DE_graph_to_dot.pl
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libexec/trinity/Analysis/DifferentialExpression/DTE_to_DTU.pl
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libexec/trinity/Analysis/DifferentialExpression/GOplot.Rscript
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libexec/trinity/Analysis/DifferentialExpression/Glimma.Trinity.Rscript
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libexec/trinity/Analysis/DifferentialExpression/PtR
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libexec/trinity/Analysis/DifferentialExpression/R/edgeR_funcs.R
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libexec/trinity/Analysis/DifferentialExpression/R/get_cluster_info.R
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libexec/trinity/Analysis/DifferentialExpression/R/heatmap.3.R
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libexec/trinity/Analysis/DifferentialExpression/R/jaccard_distance.R
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libexec/trinity/Analysis/DifferentialExpression/R/manually_define_clusters.R
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libexec/trinity/Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R
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libexec/trinity/Analysis/DifferentialExpression/R/pairs3.R
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libexec/trinity/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R
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libexec/trinity/Analysis/DifferentialExpression/R/test.heatmap.3.R
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libexec/trinity/Analysis/DifferentialExpression/R/tests/test_heatmap_w_pca.R
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libexec/trinity/Analysis/DifferentialExpression/R/vioplot2.R
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libexec/trinity/Analysis/DifferentialExpression/ROKU.pl
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libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/DE_graph_to_dot.pl
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libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/DE_results_to_pairwise_summary.pl
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libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/README.md
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libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl
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libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/pairwise_DE_summary_to_DE_classification.pl
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libexec/trinity/Analysis/DifferentialExpression/add_annot_to_trans_id.pl
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libexec/trinity/Analysis/DifferentialExpression/add_annotations_to_GO_and_lengths_file.R
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libexec/trinity/Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl
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libexec/trinity/Analysis/DifferentialExpression/analyze_diff_expr.pl
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libexec/trinity/Analysis/DifferentialExpression/assign_tissue_specific.pl
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libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/Islam_scde_data/es.mef.fpkm.matrix
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libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
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libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/cleanme.pl
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libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/orig.samples.txt
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libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/runMe.sh
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libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/samples.txt
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libexec/trinity/Analysis/DifferentialExpression/compare_gene_trans_DE_ranks.pl
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libexec/trinity/Analysis/DifferentialExpression/cut_tree_into_clusters.pl
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libexec/trinity/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
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libexec/trinity/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
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libexec/trinity/Analysis/DifferentialExpression/diff_express.cgi
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libexec/trinity/Analysis/DifferentialExpression/downsample_count_matrix.pl
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libexec/trinity/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
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libexec/trinity/Analysis/DifferentialExpression/filter_diff_expr.pl
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libexec/trinity/Analysis/DifferentialExpression/filter_matrix_min_sum_rowcounts.pl
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libexec/trinity/Analysis/DifferentialExpression/get_tissue_enriched_DE_one_vs_all.pl
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libexec/trinity/Analysis/DifferentialExpression/get_transcript_lengths.pl
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libexec/trinity/Analysis/DifferentialExpression/identify_diff_isoform_splicing.pl
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libexec/trinity/Analysis/DifferentialExpression/log2_transform_matrix.pl
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libexec/trinity/Analysis/DifferentialExpression/log2_transform_median_center_fpkm_matrix.pl
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libexec/trinity/Analysis/DifferentialExpression/matrix_to_gene_plots.pl
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libexec/trinity/Analysis/DifferentialExpression/merge_matrices.pl
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libexec/trinity/Analysis/DifferentialExpression/merge_subclusters.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/DE_pair_counts_to_matrix.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/EBSeq_to_pairwise_summary.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/add_counts_to_classes.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/edgeR_to_pairwise_summary.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/examine_rank_correlation.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/extract_venn_agree_from_summaries.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/mmdiff_to_pairwise_summary.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/notes
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/pairwise_DE_summary_to_DE_classification.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pair_stats.pl
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libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pl
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libexec/trinity/Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript
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libexec/trinity/Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript
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libexec/trinity/Analysis/DifferentialExpression/plot_expression_patterns.pl
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libexec/trinity/Analysis/DifferentialExpression/plot_log2FC_hist.Rscript
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libexec/trinity/Analysis/DifferentialExpression/prep_n_run_GOplot.pl
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libexec/trinity/Analysis/DifferentialExpression/prune_isoforms_fasta.pl
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libexec/trinity/Analysis/DifferentialExpression/prune_isoforms_gtf.pl
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libexec/trinity/Analysis/DifferentialExpression/rank_roku_by_expr.pl
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libexec/trinity/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
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libexec/trinity/Analysis/DifferentialExpression/rename_matrix_column_labels.pl
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libexec/trinity/Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl
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libexec/trinity/Analysis/DifferentialExpression/replicates_to_sample_averages_matrix.pl
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libexec/trinity/Analysis/DifferentialExpression/run_DE_analysis.pl
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libexec/trinity/Analysis/DifferentialExpression/run_GOseq.pl
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libexec/trinity/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
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libexec/trinity/Analysis/DifferentialExpression/stratify_diff_expression.pl
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libexec/trinity/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.make_index_html.pl
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libexec/trinity/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
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libexec/trinity/Analysis/DifferentialExpression/summarize_diff_expr_across_min_threshold_ranges.pl
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libexec/trinity/Analysis/DifferentialExpression/validate_UP_subset.Rscript
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libexec/trinity/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/R/boot.tree.R
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libexec/trinity/Analysis/FL_reconstruction_analysis/compute_oracle.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/fusion_comparisons_via_maps_files.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/get_genes_from_maps_file.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/oracle_counter.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_map_filter_with_isoforms.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl
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libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
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libexec/trinity/Analysis/GenomeViewPlugin/test.html
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libexec/trinity/Analysis/GenomeViewPlugin/test_session.html
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libexec/trinity/Analysis/GenomeViewPlugin/trinity_to_genomeview_html.pl
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libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
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libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
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libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/util/clean_bam.pl
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libexec/trinity/Analysis/SuperTranscripts/DTU/README.md
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libexec/trinity/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
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libexec/trinity/Analysis/SuperTranscripts/DTU/util/reformat_featureCounts.pl
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libexec/trinity/Analysis/SuperTranscripts/README.md
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libexec/trinity/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
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libexec/trinity/Analysis/SuperTranscripts/_misc/aln_before_after.pl
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libexec/trinity/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/DP_matrix.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/GraphCycleException.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Node_alignment.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Node_path.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/TGLOBALS.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/TGraph.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/TNode.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Topological_sort.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/Trinity_util.py
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libexec/trinity/Analysis/SuperTranscripts/pylib/__init__.py
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libexec/trinity/Butterfly/Butterfly.jar
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libexec/trinity/Chrysalis/bin/BubbleUpClustering
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libexec/trinity/Chrysalis/bin/Chrysalis
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libexec/trinity/Chrysalis/bin/CreateIwormFastaBundle
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libexec/trinity/Chrysalis/bin/GraphFromFasta
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libexec/trinity/Chrysalis/bin/QuantifyGraph
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libexec/trinity/Chrysalis/bin/ReadsToComponents.pl
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libexec/trinity/Chrysalis/bin/ReadsToTranscripts
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libexec/trinity/Inchworm/bin/FastaToDeBruijn
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libexec/trinity/Inchworm/bin/fastaToKmerCoverageStats
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libexec/trinity/Inchworm/bin/inchworm
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libexec/trinity/PerlLib/Ascii_genome_illustrator.pm
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libexec/trinity/PerlLib/BED_utils.pm
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libexec/trinity/PerlLib/BHStats.pm
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libexec/trinity/PerlLib/CDNA/Alignment_segment.pm
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libexec/trinity/PerlLib/CDNA/Alternative_splice_comparer.pm
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libexec/trinity/PerlLib/CDNA/CDNA_alignment.pm
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libexec/trinity/PerlLib/CDNA/CDNA_stitcher.pm
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libexec/trinity/PerlLib/CDNA/Gene_obj_alignment_assembler.pm
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libexec/trinity/PerlLib/CDNA/Genome_based_cDNA_assembler.pm
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libexec/trinity/PerlLib/CDNA/Genome_based_cDNA_graph_assembler.pm
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libexec/trinity/PerlLib/CDNA/Overlap_assembler.pm
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libexec/trinity/PerlLib/CDNA/PASA_alignment_assembler.pm
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libexec/trinity/PerlLib/CDNA/Splice_graph_assembler.pm
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libexec/trinity/PerlLib/CIGAR.pm
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libexec/trinity/PerlLib/CMD_processor.pm
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libexec/trinity/PerlLib/COMMON.pm
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libexec/trinity/PerlLib/CanvasXpress/Heatmap.pm
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libexec/trinity/PerlLib/ColorGradient.pm
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libexec/trinity/PerlLib/DelimParser.pm
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libexec/trinity/PerlLib/EM.pm
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libexec/trinity/PerlLib/Exons_to_geneobj.pm
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libexec/trinity/PerlLib/Fasta_reader.pm
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libexec/trinity/PerlLib/Fasta_retriever.pm
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libexec/trinity/PerlLib/Fastq_reader.pm
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libexec/trinity/PerlLib/GFF3_alignment_utils.pm
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libexec/trinity/PerlLib/GFF3_utils.pm
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libexec/trinity/PerlLib/GFF_maker.pm
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libexec/trinity/PerlLib/GTF.pm
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libexec/trinity/PerlLib/GTF_utils.pm
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libexec/trinity/PerlLib/Gene_obj.pm
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libexec/trinity/PerlLib/Gene_obj_indexer.pm
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libexec/trinity/PerlLib/KmerGraphLib/AlignGraph.pm
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libexec/trinity/PerlLib/KmerGraphLib/AlignNode.pm
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libexec/trinity/PerlLib/KmerGraphLib/GenericGraph.pm
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libexec/trinity/PerlLib/KmerGraphLib/GenericNode.pm
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libexec/trinity/PerlLib/KmerGraphLib/KmerGraph.pm
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libexec/trinity/PerlLib/KmerGraphLib/KmerNode.pm
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libexec/trinity/PerlLib/KmerGraphLib/ReadCoverageGraph.pm
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libexec/trinity/PerlLib/KmerGraphLib/ReadCoverageNode.pm
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libexec/trinity/PerlLib/KmerGraphLib/ReadManager.pm
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libexec/trinity/PerlLib/KmerGraphLib/ReadTracker.pm
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libexec/trinity/PerlLib/KmerGraphLib/SAM_entry.pm
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libexec/trinity/PerlLib/KmerGraphLib/SAM_reader.pm
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libexec/trinity/PerlLib/KmerGraphLib/SAM_to_AlignGraph.pm
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libexec/trinity/PerlLib/KmerGraphLib/StringGraph.pm
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libexec/trinity/PerlLib/KmerGraphLib/StringNode.pm
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libexec/trinity/PerlLib/Ktree.pm
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libexec/trinity/PerlLib/Longest_orf.pm
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libexec/trinity/PerlLib/Nuc_translator.pm
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libexec/trinity/PerlLib/Overlap_info.pm
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libexec/trinity/PerlLib/Overlap_piler.pm
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libexec/trinity/PerlLib/PSL_parser.pm
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libexec/trinity/PerlLib/Pipeliner.pm
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libexec/trinity/PerlLib/Process_cmd.pm
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libexec/trinity/PerlLib/SAM_entry.pm
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libexec/trinity/PerlLib/SAM_reader.pm
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libexec/trinity/PerlLib/Simulate/Uniform_Read_Generator.pm
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libexec/trinity/PerlLib/SingleLinkageClusterer.pm
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libexec/trinity/PerlLib/Thread_helper.pm
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libexec/trinity/PerlLib/TiedHash.pm
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libexec/trinity/PerlLib/VCF_parser.pm
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libexec/trinity/PerlLib/WigParser.pm
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libexec/trinity/PerlLib/overlapping_nucs.ph
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libexec/trinity/PerlLib/test_Fasta_retriever.pl
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libexec/trinity/PerlLib/test_htc_gridrunner_LSF.pl
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libexec/trinity/PerlLib/test_htc_gridrunner_SGE.pl
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libexec/trinity/Trinity
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libexec/trinity/trinity-plugins/BIN/seqtk-trinity
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libexec/trinity/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs
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libexec/trinity/util/PBS/N50stats.pl
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libexec/trinity/util/PBS/README
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libexec/trinity/util/PBS/TRINITY.CONFIG.template
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libexec/trinity/util/PBS/pbs_check.pl
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libexec/trinity/util/PBS/trinity_kill.pl
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libexec/trinity/util/PBS/trinity_kill.sh
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libexec/trinity/util/PBS/trinity_pbs.cont
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libexec/trinity/util/PBS/trinity_pbs.header
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libexec/trinity/util/PBS/trinity_pbs.p1
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libexec/trinity/util/PBS/trinity_pbs.p2
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libexec/trinity/util/PBS/trinity_pbs.p3
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libexec/trinity/util/PBS/trinity_pbs.p4a
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libexec/trinity/util/PBS/trinity_pbs.p4b
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libexec/trinity/util/PBS/trinity_pbs.p5b
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libexec/trinity/util/PBS/trinity_pbs.sh
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libexec/trinity/util/R/expression_analysis_lib.R
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libexec/trinity/util/R/get_Poisson_conf_intervals.R
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libexec/trinity/util/TrinityStats.pl
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libexec/trinity/util/abundance_estimates_to_matrix.pl
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libexec/trinity/util/align_and_estimate_abundance.pl
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libexec/trinity/util/analyze_blastPlus_topHit_coverage.pl
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libexec/trinity/util/filter_low_expr_transcripts.pl
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libexec/trinity/util/insilico_read_normalization.pl
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libexec/trinity/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
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libexec/trinity/util/misc/BLAT_to_SAM.pl
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libexec/trinity/util/misc/ButterflyFastaToGraphDot.pl
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libexec/trinity/util/misc/HiCpipe_nameSortedSam_to_raw.pl
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libexec/trinity/util/misc/Monarch
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libexec/trinity/util/misc/Monarch_util/generate_gene_alt_splicing_graphs.pl
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libexec/trinity/util/misc/Monarch_util/generate_trans_graphs.pl
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libexec/trinity/util/misc/N50.pl
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libexec/trinity/util/misc/PerlLib/SegmentGraph.pm
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libexec/trinity/util/misc/SAM_coordsorted_max_reads_per_position.pl
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libexec/trinity/util/misc/SAM_intron_extractor.pl
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libexec/trinity/util/misc/SAM_nameSorted_to_uniq_count_stats.pl
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libexec/trinity/util/misc/SAM_pair_to_bed.pl
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libexec/trinity/util/misc/SAM_show_alignment.pl
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libexec/trinity/util/misc/SAM_show_alignment.summarize_stats.pl
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libexec/trinity/util/misc/SAM_sortAny_to_count_stats.pl
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libexec/trinity/util/misc/SAM_toString.pl
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libexec/trinity/util/misc/SAM_to_bed.pl
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libexec/trinity/util/misc/SAM_to_fasta.pl
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libexec/trinity/util/misc/SRA_to_fastq.notes
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libexec/trinity/util/misc/SRA_to_fastq.pl
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libexec/trinity/util/misc/TEST_SUPPORT/BFLY_TESTING/graph_out_to_bfly_cmd.pl
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libexec/trinity/util/misc/TPM_weighted_gene_length.py
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libexec/trinity/util/misc/TophatCufflinksWrapper.pl
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libexec/trinity/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
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libexec/trinity/util/misc/acc_list_to_fasta_entries.pl
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libexec/trinity/util/misc/alexie_analyze_blast.pl
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libexec/trinity/util/misc/align_reads_launch_igv.pl
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libexec/trinity/util/misc/allele_simulator.pl
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libexec/trinity/util/misc/alt_GG_read_partitioning_JCornish/genwig.sh
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libexec/trinity/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py
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libexec/trinity/util/misc/altsplice_simulation_toolkit/sim_single_bubble.pl
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libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
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libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
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libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.extract_OS.pl
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libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.org_matrix.pl
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libexec/trinity/util/misc/average.pl
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libexec/trinity/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
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libexec/trinity/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
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libexec/trinity/util/misc/bam_gene_tests/harvest_transcripts.pl
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libexec/trinity/util/misc/bam_gene_tests/write_trin_cmds.pl
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libexec/trinity/util/misc/blast_outfmt6_group_segments.pl
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libexec/trinity/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
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libexec/trinity/util/misc/blast_outfmt6_group_segments.tophit_coverage.pl
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libexec/trinity/util/misc/blastn_wrapper.pl
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