577 lines
36 KiB
Text
577 lines
36 KiB
Text
@comment $NetBSD$
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bin/Trinity
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libexec/trinity/Butterfly/Butterfly.jar
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libexec/trinity/Chrysalis/BreakTransByPairs
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libexec/trinity/Chrysalis/checkLock
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libexec/trinity/Chrysalis/Chrysalis
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libexec/trinity/Chrysalis/CreateIwormFastaBundle
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libexec/trinity/Chrysalis/GraphFromFasta
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libexec/trinity/Chrysalis/GraphFromFasta_MPI
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libexec/trinity/Chrysalis/IsoformAugment
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libexec/trinity/Chrysalis/JoinTransByPairs
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libexec/trinity/Chrysalis/QuantifyGraph
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libexec/trinity/Chrysalis/ReadsToComponents.pl
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libexec/trinity/Chrysalis/ReadsToTranscripts
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libexec/trinity/Chrysalis/ReadsToTranscripts_MPI
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libexec/trinity/Chrysalis/ReadsToTranscripts_MPI_chang
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libexec/trinity/Chrysalis/RunButterfly
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libexec/trinity/Chrysalis/TranscriptomeFromVaryK
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libexec/trinity/Inchworm/bin/cigar_tweaker
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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/Inchworm/bin/pull_reads_with_kmers
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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/CanvasXpress/Heatmap.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/ColorGradient.pm
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libexec/trinity/PerlLib/COMMON.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/Gene_obj_indexer.pm
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libexec/trinity/PerlLib/Gene_obj.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/HPC/Base_handler.pm
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libexec/trinity/PerlLib/HPC/FarmIt.pm
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libexec/trinity/PerlLib/HPC/GridRunner.pm
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libexec/trinity/PerlLib/HPC/LSF_handler.pm
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libexec/trinity/PerlLib/HPC/PBS_handler.pm
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libexec/trinity/PerlLib/HPC/SGE_handler.pm
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libexec/trinity/PerlLib/HPC/SLURM_handler.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/overlapping_nucs.ph
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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/PSL_parser.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/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/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/trinity-plugins/collectl/bin/client.pl
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libexec/trinity/trinity-plugins/collectl/bin/col2tlviz.pl
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libexec/trinity/trinity-plugins/collectl/bin/collectl
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libexec/trinity/trinity-plugins/collectl/bin/collectl2html
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libexec/trinity/trinity-plugins/collectl/bin/collectl.conf
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libexec/trinity/trinity-plugins/collectl/bin/envrules.std
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libexec/trinity/trinity-plugins/collectl/bin/formatit.ph
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libexec/trinity/trinity-plugins/collectl/bin/gexpr.ph
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libexec/trinity/trinity-plugins/collectl/bin/graphite.ph
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libexec/trinity/trinity-plugins/collectl/bin/hello.ph
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libexec/trinity/trinity-plugins/collectl/bin/lexpr.ph
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libexec/trinity/trinity-plugins/collectl/bin/make_data_files.py
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libexec/trinity/trinity-plugins/collectl/bin/misc.ph
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libexec/trinity/trinity-plugins/collectl/bin/plot.py
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libexec/trinity/trinity-plugins/collectl/bin/proctree.ph
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libexec/trinity/trinity-plugins/collectl/bin/timetable.py
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libexec/trinity/trinity-plugins/collectl/bin/UNINSTALL
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libexec/trinity/trinity-plugins/collectl/bin/vmstat.ph
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libexec/trinity/trinity-plugins/GAL_0.2.1/fasta_tool
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libexec/trinity/trinity-plugins/GAL_0.2.1/README
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libexec/trinity/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs
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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/bowtie_PE_separate_then_join.pl
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libexec/trinity/util/deprecated/alignReads.pl
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libexec/trinity/util/deprecated/annot_genome_SAM_to_transcript_FPKM_simple.pl
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libexec/trinity/util/deprecated/annot_genome_SAM_to_transcriptome_SAM.pl
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libexec/trinity/util/deprecated/blastn_illumina_to_SAM.pl
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libexec/trinity/util/deprecated/cigar_tweaker.pl
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libexec/trinity/util/deprecated/cmd_process_forker.pl
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libexec/trinity/util/deprecated/csfastX_to_defastA.pl
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libexec/trinity/util/deprecated/distribute_sam_aligned_reads.pl
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libexec/trinity/util/deprecated/eXpress_util/filter_contigs.py
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libexec/trinity/util/deprecated/eXpress_util/merge_eXpress_frag_counts_single_table.pl
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libexec/trinity/util/deprecated/eXpress_util/run_eXpress_align_n_estimate.pl
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libexec/trinity/util/deprecated/eXpress_util/usage.txt
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libexec/trinity/util/deprecated/eXpress_util/use_express.py
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libexec/trinity/util/deprecated/fasta_to_deBruijn_graph.pl
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libexec/trinity/util/deprecated/PairPathsToGraphDot.pl
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libexec/trinity/util/deprecated/purge_dir.pl
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libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
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libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_frag_counts_single_table.pl
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libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_output_to_matrix.pl
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libexec/trinity/util/deprecated/RSEM_util/Nx_rsem_to_table.pl
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libexec/trinity/util/deprecated/RSEM_util/run_RSEM_align_n_estimate.pl
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libexec/trinity/util/deprecated/run_AllpathsLG_error_correction.pl
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libexec/trinity/util/deprecated/sort_fasta.sh
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libexec/trinity/util/deprecated/write_inchworm_cmds.pl
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libexec/trinity/util/fasta_tool
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libexec/trinity/util/filter_fasta_by_rsem_values.pl
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libexec/trinity/util/insilico_read_normalization.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/allele_simulator.pl
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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/Artemis/join_multi_wig_to_graph_plot.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/blastn_wrapper.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/BLAT_to_SAM.pl
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libexec/trinity/util/misc/blat_util/blat_sam_add_reads2.pl
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libexec/trinity/util/misc/blat_util/blat_top_hit_extractor.pl
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libexec/trinity/util/misc/blat_util/blat_to_sam.pl
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libexec/trinity/util/misc/blat_util/process_BLAT_alignments.pl
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libexec/trinity/util/misc/blat_util/pslx_to_gff3.pl
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libexec/trinity/util/misc/blat_util/run_BLAT_shortReads.pl
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libexec/trinity/util/misc/blat_util/top_blat_sam_extractor.pl
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libexec/trinity/util/misc/ButterflyFastaToGraphDot.pl
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libexec/trinity/util/misc/capture_orig_n_unmapped_reads.pl
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libexec/trinity/util/misc/cat_require_newlines.pl
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libexec/trinity/util/misc/cdna_fasta_file_to_transcript_gtf.pl
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libexec/trinity/util/misc/check_fastQ_pair_ordering.pl
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libexec/trinity/util/misc/chrys_graph_to_dot.pl
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libexec/trinity/util/misc/combined_nameSorted_to_dup_pairs_removed.pl
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libexec/trinity/util/misc/compare_bflies.pl
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libexec/trinity/util/misc/component_to_graph_dot.pl
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libexec/trinity/util/misc/contig_ExN50_statistic.pl
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libexec/trinity/util/misc/convert_fasta_identifiers_for_FL_analysis.pl
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libexec/trinity/util/misc/count_features_given_MIN_FPKM_threshold.pl
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libexec/trinity/util/misc/count_iso_per_gene_dist.pl
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libexec/trinity/util/misc/count_matrix_features_given_MIN_TPM_threshold.pl
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libexec/trinity/util/misc/count_N50_given_MIN_FPKM_threshold.pl
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libexec/trinity/util/misc/count_number_fasta_seqs.pl
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libexec/trinity/util/misc/count_trans_per_component.pl
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libexec/trinity/util/misc/decode_SAM_flag_value.pl
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libexec/trinity/util/misc/describe_SAM_read_flag_info.pl
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libexec/trinity/util/misc/examine_iworm_FL_across_threads.pl
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libexec/trinity/util/misc/examine_weldmer_halves.pl
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libexec/trinity/util/misc/extract_fastQ_pairings.pl
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libexec/trinity/util/misc/fan_out_fasta_seqs_to_indiv_files.pl
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libexec/trinity/util/misc/fasta_file_reformatter.pl
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libexec/trinity/util/misc/fasta_filter_by_min_length.pl
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libexec/trinity/util/misc/fasta_remove_duplicates.pl
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libexec/trinity/util/misc/fasta_to_cmd_generator.pl
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libexec/trinity/util/misc/fasta_write_sense_n_anti.pl
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libexec/trinity/util/misc/fastQ_append_acc.pl
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libexec/trinity/util/misc/fastq_cleaner.pl
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libexec/trinity/util/misc/fastq_interleave_pairs.pl
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libexec/trinity/util/misc/fastq_merge_sorted_tab_lists.pl
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libexec/trinity/util/misc/fastQ_rand_subset.pl
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libexec/trinity/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
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libexec/trinity/util/misc/fastq_stats.pl
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libexec/trinity/util/misc/fastQ_top_N_records.pl
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libexec/trinity/util/misc/fastq_unweave_pairs.pl
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libexec/trinity/util/misc/frag_boundary_to_wig.pl
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libexec/trinity/util/misc/frag_to_bed.pl
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libexec/trinity/util/misc/gene_gff3_to_introns.pl
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libexec/trinity/util/misc/gene_to_shared_transcript_content.pl
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libexec/trinity/util/misc/genome_gff3_to_gene_gff3_partitions.pl
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libexec/trinity/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
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libexec/trinity/util/misc/get_path_nodes_from_fasta.pl
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libexec/trinity/util/misc/get_welds_from_chrysals_graphFromFasta_out.pl
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libexec/trinity/util/misc/gff3_file_to_cdna.pl
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libexec/trinity/util/misc/gff3_file_utr_coverage_trimmer.pl
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libexec/trinity/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
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libexec/trinity/util/misc/gff3_to_genome_feature_base_encoding.pl
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libexec/trinity/util/misc/gmap_gff3_chimera_jaccard_analyzer.pl
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libexec/trinity/util/misc/gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
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libexec/trinity/util/misc/gmap_gff3_to_percent_length_stats.pl
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libexec/trinity/util/misc/gmap_native_to_format_converter.pl
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libexec/trinity/util/misc/gtf_to_bed_format.pl
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libexec/trinity/util/misc/gtf_to_introns.pl
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libexec/trinity/util/misc/HiCpipe_nameSortedSam_to_raw.pl
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libexec/trinity/util/misc/hicpipe_raw_converter.pl
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libexec/trinity/util/misc/identify_distal_isoform_variations.pl
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libexec/trinity/util/misc/illustrate_ref_comparison.pl
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libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.all.txt
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libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.NormMaxKCov50.txt
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libexec/trinity/util/misc/insilico_norm_kmer_hists/plot_me.R
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libexec/trinity/util/misc/insilico_norm_kmer_hists/result.pdf
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libexec/trinity/util/misc/iso_reco_analysis/bam_to_cuff.pl
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libexec/trinity/util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl
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libexec/trinity/util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl
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libexec/trinity/util/misc/iso_reco_analysis/gmap_to_ref.pl
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libexec/trinity/util/misc/iso_reco_analysis/notes
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libexec/trinity/util/misc/iso_reco_analysis/run_trinity_no_LR.pl
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libexec/trinity/util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl
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libexec/trinity/util/misc/iso_reco_analysis/sim_reads.pl
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libexec/trinity/util/misc/iso_reco_analysis/trans_gff3_to_bed_cmds.pl
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libexec/trinity/util/misc/jaccard_sam_pair_refiner.pl
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libexec/trinity/util/misc/join_any.pl
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libexec/trinity/util/misc/join_by_left_col.pl
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libexec/trinity/util/misc/join_expr_vals_single_table.pl
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libexec/trinity/util/misc/kmer_counter.pl
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libexec/trinity/util/misc/m8_blastclust.pl
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libexec/trinity/util/misc/map_gtf_transcripts_to_genome_annots.pl
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libexec/trinity/util/misc/merge_blast_n_rsem_results.pl
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libexec/trinity/util/misc/merge_rsem_n_express_for_compare.pl
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libexec/trinity/util/misc/merge_RSEM_output_to_matrix.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/mpi_iworm_proc_contigs_to_fa.pl
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libexec/trinity/util/misc/N50.pl
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libexec/trinity/util/misc/nameSorted_SAM_to_FastQ.pl
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libexec/trinity/util/misc/omp_iworm_thread_contigs_to_fa.pl
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libexec/trinity/util/misc/organize_data_table_by_trinity_component.pl
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libexec/trinity/util/misc/pair_up_fastq_files_1_2.pl
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libexec/trinity/util/misc/pair_up_fastq_files_LeftRight.pl
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libexec/trinity/util/misc/pair_up_fastq_files_R1_R2.pl
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libexec/trinity/util/misc/pairwise_kmer_content_comparer.pl
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libexec/trinity/util/misc/PerlLib/SegmentGraph.pm
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libexec/trinity/util/misc/plot_expressed_gene_dist.pl
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libexec/trinity/util/misc/print_kmers.pl
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libexec/trinity/util/misc/print.pl
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libexec/trinity/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
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libexec/trinity/util/misc/prop_pair_sam_refiner.pl
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libexec/trinity/util/misc/remove_cntrl_chars.pl
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libexec/trinity/util/misc/row_to_column.pl
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libexec/trinity/util/misc/run_bwa.pl
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libexec/trinity/util/misc/run_bwasw_trinity.pl
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libexec/trinity/util/misc/run_GSNAP.pl
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libexec/trinity/util/misc/run_HiCpipe_bowtie.pl
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libexec/trinity/util/misc/run_HISAT.pl
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libexec/trinity/util/misc/run_jellyfish.pl
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libexec/trinity/util/misc/run_read_simulator_per_fasta_entry.pl
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libexec/trinity/util/misc/run_read_simulator_per_gene.pl
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