896 lines
43 KiB
Plaintext
896 lines
43 KiB
Plaintext
@comment $NetBSD$
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bin/00_README.txt
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bin/anvi-cluster-with-concoct
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bin/anvi-compute-ani
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bin/anvi-compute-completeness
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bin/anvi-compute-gene-cluster-homogeneity
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bin/anvi-db-info
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bin/anvi-delete-collection
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bin/anvi-delete-hmms
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bin/anvi-delete-misc-data
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bin/anvi-delete-state
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bin/anvi-display-contigs-stats
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bin/anvi-display-pan
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bin/anvi-display-structure
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bin/anvi-experimental-organization
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bin/anvi-export-collection
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bin/anvi-export-contigs
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bin/anvi-export-functions
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bin/anvi-export-gene-calls
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bin/anvi-export-gene-coverage-and-detection
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bin/anvi-export-locus
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bin/anvi-export-misc-data
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bin/anvi-export-splits-and-coverages
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bin/anvi-export-splits-taxonomy
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bin/anvi-export-state
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bin/anvi-export-table
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bin/anvi-gen-contigs-database
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bin/anvi-gen-gene-consensus-sequences
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bin/anvi-gen-genomes-storage
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bin/anvi-gen-network
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bin/anvi-gen-phylogenomic-tree
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bin/anvi-gen-structure-database
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bin/anvi-gen-variability-matrix
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bin/anvi-gen-variability-network
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bin/anvi-gen-variability-profile
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bin/anvi-get-aa-counts
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bin/anvi-get-codon-frequencies
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bin/anvi-get-enriched-functions-per-pan-group
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bin/anvi-get-sequences-for-gene-calls
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bin/anvi-get-sequences-for-gene-clusters
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bin/anvi-get-sequences-for-hmm-hits
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bin/anvi-get-short-reads-from-bam
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bin/anvi-get-short-reads-mapping-to-a-gene
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bin/anvi-get-split-coverages
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bin/anvi-import-collection
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bin/anvi-import-functions
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bin/anvi-import-misc-data
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bin/anvi-import-state
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bin/anvi-import-taxonomy-for-genes
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bin/anvi-import-taxonomy-for-layers
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bin/anvi-init-bam
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bin/anvi-interactive
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bin/anvi-matrix-to-newick
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bin/anvi-mcg-classifier
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bin/anvi-merge
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bin/anvi-merge-bins
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bin/anvi-meta-pan-genome
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bin/anvi-migrate-db
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bin/anvi-oligotype-linkmers
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bin/anvi-pan-genome
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bin/anvi-profile
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bin/anvi-push
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bin/anvi-refine
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bin/anvi-rename-bins
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bin/anvi-report-linkmers
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bin/anvi-run-hmms
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bin/anvi-run-ncbi-cogs
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bin/anvi-run-pfams
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bin/anvi-run-workflow
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bin/anvi-saavs-and-protein-structures-summary
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bin/anvi-script-FASTA-to-contigs-db
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bin/anvi-script-add-default-collection
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bin/anvi-script-calculate-pn-ps-ratio
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bin/anvi-script-checkm-tree-to-interactive
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bin/anvi-script-compute-ani-for-fasta
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bin/anvi-script-filter-fasta-by-blast
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bin/anvi-script-gen-CPR-classifier
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bin/anvi-script-gen-distribution-of-genes-in-a-bin
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bin/anvi-script-gen-hmm-hits-matrix-across-genomes
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bin/anvi-script-gen-programs-network
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bin/anvi-script-gen-programs-vignette
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bin/anvi-script-gen-short-reads
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bin/anvi-script-gen_stats_for_single_copy_genes.R
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bin/anvi-script-gen_stats_for_single_copy_genes.README
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bin/anvi-script-gen_stats_for_single_copy_genes.py
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bin/anvi-script-gen_stats_for_single_copy_genes.sh
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bin/anvi-script-genbank-to-external-gene-calls
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bin/anvi-script-get-collection-info
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bin/anvi-script-merge-collections
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bin/anvi-script-predict-CPR-genomes
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bin/anvi-script-reformat-fasta
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bin/anvi-script-run-eggnog-mapper
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bin/anvi-script-snvs-to-interactive
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bin/anvi-script-transpose-matrix
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bin/anvi-search-functions
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bin/anvi-self-test
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bin/anvi-setup-ncbi-cogs
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bin/anvi-setup-pfams
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bin/anvi-show-collections-and-bins
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bin/anvi-show-misc-data
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bin/anvi-split
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bin/anvi-summarize
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bin/anvi-update-db-description
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bin/anvi-update-genes-in-structure-database
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${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
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${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
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${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
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${PYSITELIB}/${EGG_INFODIR}/requires.txt
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${PYSITELIB}/${EGG_INFODIR}/top_level.txt
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${PYSITELIB}/anvio/__init__.py
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${PYSITELIB}/anvio/__init__.pyo
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${PYSITELIB}/anvio/__init__.pyc
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${PYSITELIB}/anvio/auxiliarydataops.pyo
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${PYSITELIB}/anvio/auxiliarydataops.pyc
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${PYSITELIB}/anvio/bamops.pyo
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${PYSITELIB}/anvio/bamops.pyc
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${PYSITELIB}/anvio/bottleroutes.pyo
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${PYSITELIB}/anvio/bottleroutes.pyc
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${PYSITELIB}/anvio/ccollections.pyo
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${PYSITELIB}/anvio/ccollections.pyc
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${PYSITELIB}/anvio/clustering.pyo
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${PYSITELIB}/anvio/clustering.pyc
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${PYSITELIB}/anvio/clusteringconfuguration.pyo
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${PYSITELIB}/anvio/clusteringconfuguration.pyc
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${PYSITELIB}/anvio/cogs.pyo
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${PYSITELIB}/anvio/cogs.pyc
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${PYSITELIB}/anvio/completeness.pyo
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${PYSITELIB}/anvio/completeness.pyc
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${PYSITELIB}/anvio/concoct.pyo
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${PYSITELIB}/anvio/concoct.pyc
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${PYSITELIB}/anvio/constants.pyo
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${PYSITELIB}/anvio/constants.pyc
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${PYSITELIB}/anvio/contigops.pyo
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${PYSITELIB}/anvio/contigops.pyc
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${PYSITELIB}/anvio/db.pyo
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${PYSITELIB}/anvio/db.pyc
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${PYSITELIB}/anvio/dbops.pyo
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${PYSITELIB}/anvio/dbops.pyc
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${PYSITELIB}/anvio/dictio.pyo
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${PYSITELIB}/anvio/dictio.pyc
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${PYSITELIB}/anvio/errors.pyo
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${PYSITELIB}/anvio/errors.pyc
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${PYSITELIB}/anvio/fastalib.pyo
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${PYSITELIB}/anvio/fastalib.pyc
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${PYSITELIB}/anvio/filesnpaths.pyo
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${PYSITELIB}/anvio/filesnpaths.pyc
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${PYSITELIB}/anvio/genecalling.pyo
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${PYSITELIB}/anvio/genecalling.pyc
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${PYSITELIB}/anvio/genomedescriptions.pyo
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${PYSITELIB}/anvio/genomedescriptions.pyc
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${PYSITELIB}/anvio/genomestorage.pyo
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${PYSITELIB}/anvio/genomestorage.pyc
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${PYSITELIB}/anvio/hmmops.pyo
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${PYSITELIB}/anvio/hmmops.pyc
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${PYSITELIB}/anvio/hmmopswrapper.pyo
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${PYSITELIB}/anvio/hmmopswrapper.pyc
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${PYSITELIB}/anvio/homogeneityindex.pyo
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${PYSITELIB}/anvio/homogeneityindex.pyc
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${PYSITELIB}/anvio/interactive.pyo
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${PYSITELIB}/anvio/interactive.pyc
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${PYSITELIB}/anvio/kmers.pyo
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${PYSITELIB}/anvio/kmers.pyc
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${PYSITELIB}/anvio/learning.pyo
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${PYSITELIB}/anvio/learning.pyc
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${PYSITELIB}/anvio/mcgclassifier.pyo
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${PYSITELIB}/anvio/mcgclassifier.pyc
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${PYSITELIB}/anvio/mcgops.pyo
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${PYSITELIB}/anvio/mcgops.pyc
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${PYSITELIB}/anvio/merger.pyo
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${PYSITELIB}/anvio/merger.pyc
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${PYSITELIB}/anvio/metapanops.pyo
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${PYSITELIB}/anvio/metapanops.pyc
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${PYSITELIB}/anvio/panops.pyo
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${PYSITELIB}/anvio/panops.pyc
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${PYSITELIB}/anvio/pfam.pyo
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${PYSITELIB}/anvio/pfam.pyc
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${PYSITELIB}/anvio/profiler.pyo
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${PYSITELIB}/anvio/profiler.pyc
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${PYSITELIB}/anvio/programs.pyo
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${PYSITELIB}/anvio/programs.pyc
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${PYSITELIB}/anvio/samplesops.pyo
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${PYSITELIB}/anvio/samplesops.pyc
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${PYSITELIB}/anvio/sequence.pyo
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${PYSITELIB}/anvio/sequence.pyc
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${PYSITELIB}/anvio/serverAPI.pyo
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${PYSITELIB}/anvio/serverAPI.pyc
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${PYSITELIB}/anvio/sge.pyo
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${PYSITELIB}/anvio/sge.pyc
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${PYSITELIB}/anvio/splitter.pyo
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${PYSITELIB}/anvio/splitter.pyc
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${PYSITELIB}/anvio/structureops.pyo
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${PYSITELIB}/anvio/structureops.pyc
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${PYSITELIB}/anvio/summarizer.pyo
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${PYSITELIB}/anvio/summarizer.pyc
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${PYSITELIB}/anvio/summaryhtml.pyo
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${PYSITELIB}/anvio/summaryhtml.pyc
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${PYSITELIB}/anvio/terminal.pyo
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${PYSITELIB}/anvio/terminal.pyc
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${PYSITELIB}/anvio/ttycolors.pyo
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${PYSITELIB}/anvio/ttycolors.pyc
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${PYSITELIB}/anvio/utils.pyo
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${PYSITELIB}/anvio/utils.pyc
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${PYSITELIB}/anvio/variability.pyo
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${PYSITELIB}/anvio/variability.pyc
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${PYSITELIB}/anvio/variabilityops.pyo
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${PYSITELIB}/anvio/variabilityops.pyc
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${PYSITELIB}/anvio/auxiliarydataops.py
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${PYSITELIB}/anvio/bamops.py
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${PYSITELIB}/anvio/bottleroutes.py
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${PYSITELIB}/anvio/ccollections.py
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${PYSITELIB}/anvio/clustering.py
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${PYSITELIB}/anvio/clusteringconfuguration.py
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${PYSITELIB}/anvio/cogs.py
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${PYSITELIB}/anvio/completeness.py
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${PYSITELIB}/anvio/concoct.py
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${PYSITELIB}/anvio/constants.py
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${PYSITELIB}/anvio/contigops.py
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${PYSITELIB}/anvio/data/SSMs/AA/BLOSUM62.txt
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${PYSITELIB}/anvio/data/SSMs/AA/BLOSUM90.txt
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${PYSITELIB}/anvio/data/SSMs/AA/__init__.py
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${PYSITELIB}/anvio/data/SSMs/AA/__init__.pyo
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${PYSITELIB}/anvio/data/SSMs/AA/__init__.pyc
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${PYSITELIB}/anvio/data/SSMs/CDN/__init__.py
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${PYSITELIB}/anvio/data/SSMs/CDN/__init__.pyo
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${PYSITELIB}/anvio/data/SSMs/CDN/__init__.pyc
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${PYSITELIB}/anvio/data/SSMs/NT/__init__.py
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${PYSITELIB}/anvio/data/SSMs/NT/__init__.pyo
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${PYSITELIB}/anvio/data/SSMs/NT/__init__.pyc
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${PYSITELIB}/anvio/data/SSMs/README.md
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${PYSITELIB}/anvio/data/SSMs/__init__.py
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${PYSITELIB}/anvio/data/SSMs/__init__.pyo
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${PYSITELIB}/anvio/data/SSMs/__init__.pyc
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${PYSITELIB}/anvio/data/__init__.py
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${PYSITELIB}/anvio/data/__init__.pyo
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${PYSITELIB}/anvio/data/__init__.pyc
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${PYSITELIB}/anvio/data/clusterconfigs/README.md
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${PYSITELIB}/anvio/data/clusterconfigs/blank/tnf
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${PYSITELIB}/anvio/data/clusterconfigs/blank/tnf-splits
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${PYSITELIB}/anvio/data/clusterconfigs/merged/cov
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${PYSITELIB}/anvio/data/clusterconfigs/merged/tnf
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${PYSITELIB}/anvio/data/clusterconfigs/merged/tnf-cov
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${PYSITELIB}/anvio/data/clusterconfigs/pan/frequency
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${PYSITELIB}/anvio/data/clusterconfigs/pan/presence-absence
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${PYSITELIB}/anvio/data/clusterconfigs/single/tnf
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${PYSITELIB}/anvio/data/clusterconfigs/single/tnf-ab-cov
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${PYSITELIB}/anvio/data/hmm/BUSCO_83_Protista/genes.hmm.gz
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${PYSITELIB}/anvio/data/hmm/BUSCO_83_Protista/genes.txt
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${PYSITELIB}/anvio/data/hmm/BUSCO_83_Protista/kind.txt
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${PYSITELIB}/anvio/data/hmm/BUSCO_83_Protista/noise_cutoff_terms.txt
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${PYSITELIB}/anvio/data/hmm/BUSCO_83_Protista/reference.txt
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${PYSITELIB}/anvio/data/hmm/BUSCO_83_Protista/target.txt
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${PYSITELIB}/anvio/data/hmm/Campbell_et_al/genes.hmm.gz
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${PYSITELIB}/anvio/data/hmm/Campbell_et_al/genes.txt
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${PYSITELIB}/anvio/data/hmm/Campbell_et_al/kind.txt
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${PYSITELIB}/anvio/data/hmm/Campbell_et_al/noise_cutoff_terms.txt
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${PYSITELIB}/anvio/data/hmm/Campbell_et_al/reference.txt
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${PYSITELIB}/anvio/data/hmm/Campbell_et_al/target.txt
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${PYSITELIB}/anvio/data/hmm/Ribosomal_RNAs/README.md
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${PYSITELIB}/anvio/data/hmm/Ribosomal_RNAs/genes.hmm.gz
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${PYSITELIB}/anvio/data/hmm/Ribosomal_RNAs/genes.txt
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${PYSITELIB}/anvio/data/hmm/Ribosomal_RNAs/kind.txt
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${PYSITELIB}/anvio/data/hmm/Ribosomal_RNAs/noise_cutoff_terms.txt
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${PYSITELIB}/anvio/data/hmm/Ribosomal_RNAs/reference.txt
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${PYSITELIB}/anvio/data/hmm/Ribosomal_RNAs/target.txt
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${PYSITELIB}/anvio/data/hmm/Rinke_et_al/genes.hmm.gz
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${PYSITELIB}/anvio/data/hmm/Rinke_et_al/genes.txt
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${PYSITELIB}/anvio/data/hmm/Rinke_et_al/kind.txt
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${PYSITELIB}/anvio/data/hmm/Rinke_et_al/noise_cutoff_terms.txt
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${PYSITELIB}/anvio/data/hmm/Rinke_et_al/reference.txt
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${PYSITELIB}/anvio/data/hmm/Rinke_et_al/target.txt
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${PYSITELIB}/anvio/data/hmm/__init__.py
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${PYSITELIB}/anvio/data/hmm/__init__.pyo
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${PYSITELIB}/anvio/data/hmm/__init__.pyc
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${PYSITELIB}/anvio/data/interactive/charts.html
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${PYSITELIB}/anvio/data/interactive/contigs.html
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${PYSITELIB}/anvio/data/interactive/css/charts.css
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${PYSITELIB}/anvio/data/interactive/css/contigs-plot.css
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${PYSITELIB}/anvio/data/interactive/css/geneclusters.css
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${PYSITELIB}/anvio/data/interactive/css/glowing-button.css
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${PYSITELIB}/anvio/data/interactive/css/loading.css
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${PYSITELIB}/anvio/data/interactive/css/main.css
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${PYSITELIB}/anvio/data/interactive/css/markdown-local.css
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${PYSITELIB}/anvio/data/interactive/css/normalize.css
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${PYSITELIB}/anvio/data/interactive/css/popover.css
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${PYSITELIB}/anvio/data/interactive/css/structure.css
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${PYSITELIB}/anvio/data/interactive/geneclusters.html
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${PYSITELIB}/anvio/data/interactive/images/blank.gif
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${PYSITELIB}/anvio/data/interactive/images/collection-bg.png
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${PYSITELIB}/anvio/data/interactive/images/custom_indic.gif
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${PYSITELIB}/anvio/data/interactive/images/drag.gif
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${PYSITELIB}/anvio/data/interactive/images/fractal.jpg
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${PYSITELIB}/anvio/data/interactive/images/full-bg.png
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${PYSITELIB}/anvio/data/interactive/images/gene-bg.png
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${PYSITELIB}/anvio/data/interactive/images/loading.gif
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${PYSITELIB}/anvio/data/interactive/images/logo-simple.png
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${PYSITELIB}/anvio/data/interactive/images/logo.png
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${PYSITELIB}/anvio/data/interactive/images/manual-bg.png
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${PYSITELIB}/anvio/data/interactive/images/pan-bg.png
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${PYSITELIB}/anvio/data/interactive/images/peaceful.jpg
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${PYSITELIB}/anvio/data/interactive/images/refine-bg.png
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${PYSITELIB}/anvio/data/interactive/images/server-bg.png
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${PYSITELIB}/anvio/data/interactive/images/spinning_dna.gif
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${PYSITELIB}/anvio/data/interactive/index.html
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${PYSITELIB}/anvio/data/interactive/js/animations.js
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${PYSITELIB}/anvio/data/interactive/js/area-zoom.js
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${PYSITELIB}/anvio/data/interactive/js/bin.js
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${PYSITELIB}/anvio/data/interactive/js/charts.js
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${PYSITELIB}/anvio/data/interactive/js/color-coding.js
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${PYSITELIB}/anvio/data/interactive/js/constants.js
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${PYSITELIB}/anvio/data/interactive/js/context-menu.js
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${PYSITELIB}/anvio/data/interactive/js/contigs-plot.js
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${PYSITELIB}/anvio/data/interactive/js/dialogs/collapse-node.js
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${PYSITELIB}/anvio/data/interactive/js/dialogs/load-collection.js
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${PYSITELIB}/anvio/data/interactive/js/dialogs/save-tree.js
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${PYSITELIB}/anvio/data/interactive/js/dialogs/store-collection.js
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${PYSITELIB}/anvio/data/interactive/js/drawer.js
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${PYSITELIB}/anvio/data/interactive/js/geneclusters.js
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${PYSITELIB}/anvio/data/interactive/js/help-messages.js
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${PYSITELIB}/anvio/data/interactive/js/inspectionutils.js
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${PYSITELIB}/anvio/data/interactive/js/main.js
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${PYSITELIB}/anvio/data/interactive/js/migrations.js
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${PYSITELIB}/anvio/data/interactive/js/mouse-events.js
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${PYSITELIB}/anvio/data/interactive/js/multiple.js
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${PYSITELIB}/anvio/data/interactive/js/news.js
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${PYSITELIB}/anvio/data/interactive/js/sample.js
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${PYSITELIB}/tests/sandbox/mock_data_for_structure/one_contig_five_genes.fa
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${PYSITELIB}/tests/sandbox/mock_data_for_structure/proteins.fa
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/TEST-COLLECTION.txt
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/TEST.fa
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/default.json
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/hmp0041-RAW.bam
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/hmp0062-RAW.bam
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/hmp0074-RAW.bam
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/hmp0075-RAW.bam
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/hmp0079-RAW.bam
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/hmp0094-RAW.bam
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/samples_to_exclude.txt
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${PYSITELIB}/tests/sandbox/mock_files_for_alons_classifier/samples_to_include.txt
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${PYSITELIB}/tests/sandbox/myrast_cmdline/README.txt
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${PYSITELIB}/tests/sandbox/myrast_cmdline/svr_assign_to_dna_using_figfams.txt
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${PYSITELIB}/tests/sandbox/myrast_cmdline/svr_assign_using_figfams.txt
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${PYSITELIB}/tests/sandbox/myrast_cmdline/svr_call_pegs.txt
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${PYSITELIB}/tests/sandbox/myrast_gui/functions.tbl
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${PYSITELIB}/tests/sandbox/myrast_gui/gene_otus.tbl
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${PYSITELIB}/tests/sandbox/myrast_gui/peg.tbl
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${PYSITELIB}/tests/sandbox/sample_CONCOCT_bin_id.txt
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${PYSITELIB}/tests/sandbox/sample_contig_ids.txt
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${PYSITELIB}/tests/sandbox/sample_gene_call_ids.txt
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${PYSITELIB}/tests/sandbox/samples-information.txt
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${PYSITELIB}/tests/sandbox/samples-order.txt
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${PYSITELIB}/tests/sandbox/samples-single-order-basic.txt
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${PYSITELIB}/tests/sandbox/samples-single-order-newick.txt
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${PYSITELIB}/tests/sandbox/samples_to_exclude_for_mcg.txt
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${PYSITELIB}/tests/sandbox/samples_to_include_for_mcg.txt
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${PYSITELIB}/tests/sandbox/single_contig.fa
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${PYSITELIB}/tests/sandbox/smtp_config_sample.ini
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${PYSITELIB}/tests/sandbox/workflows/contigs/fasta.txt
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/config-idba_ud-no-qc.json
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/config-idba_ud.json
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/config-megahit-no-qc-all-against-all.json
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/config-megahit.json
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/config-references-mode-no-qc-no-gzip-no-groups.json
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/config-references-mode.json
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/fasta.txt
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/kraken.txt
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/sample_01.krakenhll_tax
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/sample_02.krakenhll_tax
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/sample_03.krakenhll_tax
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/samples-for-idba_ud.txt
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/samples-no-groups.txt
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/samples.txt
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/three_samples_example/G01-contigs.fa.gz
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/three_samples_example/G02-contigs.fa.gz
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/three_samples_example/sample-01-R1.fastq.gz
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/three_samples_example/sample-01-R2.fastq.gz
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/three_samples_example/sample-02-R1.fastq.gz
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/three_samples_example/sample-02-R2.fastq.gz
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/three_samples_example/sample-03-R1.fastq.gz
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${PYSITELIB}/tests/sandbox/workflows/metagenomics/three_samples_example/sample-03-R2.fastq.gz
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${PYSITELIB}/tests/sandbox/workflows/pangenomics/config.json
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${PYSITELIB}/tests/server/README.txt
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${PYSITELIB}/tests/server/run_server_tests.pyo
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${PYSITELIB}/tests/server/run_server_tests.pyc
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${PYSITELIB}/tests/server/run_server_tests.py
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${PYSITELIB}/tests/server/start_server.sh
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${PYSITELIB}/tests/test-mcg-classifier/config.json
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${PYSITELIB}/tests/test-mcg-classifier/mcg-classifier.snakefile
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