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anvi-cluster-with-concoct
anvi-compute-ani
anvi-compute-completeness
anvi-compute-gene-cluster-homogeneity
anvi-db-info
anvi-delete-collection
anvi-delete-hmms
anvi-delete-misc-data
anvi-delete-state
anvi-display-contigs-stats
anvi-display-pan
anvi-display-structure
anvi-experimental-organization
anvi-export-collection
anvi-export-contigs
anvi-export-functions
anvi-export-gene-calls
anvi-export-gene-coverage-and-detection
anvi-export-locus
anvi-export-misc-data
anvi-export-splits-and-coverages
anvi-export-splits-taxonomy
anvi-export-state
anvi-export-table
anvi-gen-contigs-database
anvi-gen-gene-consensus-sequences
anvi-gen-genomes-storage
anvi-gen-network
anvi-gen-phylogenomic-tree
anvi-gen-structure-database
anvi-gen-variability-matrix
anvi-gen-variability-network
anvi-gen-variability-profile
anvi-get-aa-counts
anvi-get-codon-frequencies
anvi-get-enriched-functions-per-pan-group
anvi-get-sequences-for-gene-calls
anvi-get-sequences-for-gene-clusters
anvi-get-sequences-for-hmm-hits
anvi-get-short-reads-from-bam
anvi-get-short-reads-mapping-to-a-gene
anvi-get-split-coverages
anvi-import-collection
anvi-import-functions
anvi-import-misc-data
anvi-import-state
anvi-import-taxonomy-for-genes
anvi-import-taxonomy-for-layers
anvi-init-bam
anvi-interactive
anvi-matrix-to-newick
anvi-mcg-classifier
anvi-merge
anvi-merge-bins
anvi-meta-pan-genome
anvi-migrate-db
anvi-oligotype-linkmers
anvi-pan-genome
anvi-profile
anvi-push
anvi-refine
anvi-rename-bins
anvi-report-linkmers
anvi-run-hmms
anvi-run-ncbi-cogs
anvi-run-pfams
anvi-run-workflow
anvi-saavs-and-protein-structures-summary
anvi-search-functions
anvi-self-test
anvi-setup-ncbi-cogs
anvi-setup-pfams
anvi-show-collections-and-bins
anvi-show-misc-data
anvi-split
anvi-summarize
anvi-update-db-description
anvi-update-genes-in-structure-database