MAAGE Command Line Program Reference
- Common Options to Command Line Programs
- GenomeTypeObject
- Hsp
- P3DataAPI
- P3Utils
- Sim
- appserv-enumerate-apps
- appserv-enumerate-tasks
- appserv-kill-task
- appserv-query-task
- appserv-rerun-task
- appserv-start-app
- p3-aggregates-to-html
- p3-all-contigs
- p3-all-drugs
- p3-all-genomes
- p3-all-subsystem-roles
- p3-all-subsystems
- p3-all-taxonomies
- p3-blast
- p3-build-kmer-db
- p3-cat
- p3-closest-seqs
- p3-co-occur
- p3-collate
- p3-compare-cols
- p3-count
- p3-count-families
- p3-cp
- p3-discriminating-kmers
- p3-dump-genomes
- p3-echo
- p3-extract
- p3-fasta-md5
- p3-feature-gap
- p3-feature-upstream
- p3-file-filter
- p3-find-couples
- p3-find-features
- p3-find-in-clusters
- p3-find-serology-data
- p3-find-surveillance-data
- p3-format-results
- p3-function-parse
- p3-function-to-role
- p3-generate-close-roles
- p3-generate-clusters
- p3-genome-distance
- p3-genome-fasta
- p3-genome-kmer-hits
- p3-genome-md5
- p3-genus-species
- p3-get-drug-genomes
- p3-get-family-data
- p3-get-family-features
- p3-get-feature-data
- p3-get-feature-group
- p3-get-feature-protein-regions
- p3-get-feature-protein-structures
- p3-get-feature-regions
- p3-get-feature-sequence
- p3-get-feature-subsystems
- p3-get-features-by-sequence
- p3-get-features-in-regions
- p3-get-genome-contigs
- p3-get-genome-data
- p3-get-genome-drugs
- p3-get-genome-expression
- p3-get-genome-features
- p3-get-genome-group
- p3-get-genome-protein-regions
- p3-get-genome-protein-structures
- p3-get-genome-refseq-features
- p3-get-genome-sp-genes
- p3-get-genome-subsystems
- p3-get-subsystem-features
- p3-get-subsystem-roles
- p3-get-taxonomy-data
- p3-gto
- p3-gto-dna
- p3-gto-fasta
- p3-gto-fetch
- p3-gto-scan
- p3-head
- p3-identify-clusters
- p3-job-status
- p3-join
- p3-kmer-compare
- p3-less
- p3-list-feature-groups
- p3-list-genome-groups
- p3-login
- p3-logout
- p3-ls
- p3-mass-cluster-run
- p3-match
- p3-merge
- p3-mkdir
- p3-nucleon-runs
- p3-peg-kmer-hits
- p3-pick
- p3-pick-by-class
- p3-pivot
- p3-project-subsystems
- p3-put-feature-group
- p3-put-genome-group
- p3-qstat
- p3-rast
- p3-related-by-clusters
- p3-rep-prots
- p3-rm
- p3-rmdir
- p3-role-fasta
- p3-role-features
- p3-role-matrix
- p3-sequence-profile
- p3-set-to-relation
- p3-shuffle
- p3-signature-clusters
- p3-signature-families
- p3-signature-peginfo
- p3-sort
- p3-stats
- p3-submit-BLAST
- p3-submit-CGA
- p3-submit-MSA
- p3-submit-codon-tree
- p3-submit-fastqutils
- p3-submit-gene-tree
- p3-submit-genome-annotation
- p3-submit-genome-assembly
- p3-submit-metagenome-binning
- p3-submit-metagenomic-read-mapping
- p3-submit-proteome-comparison
- p3-submit-rnaseq
- p3-submit-sars2-analysis
- p3-submit-sars2-assembly
- p3-submit-taxonomic-classification
- p3-submit-variation-analysis
- p3-subsys-roles
- p3-tail
- p3-tbl-to-fasta
- p3-tbl-to-html
- p3-tests
- p3-uni-roles
- p3-user-subsystem
- p3-whoami
- p3-write-kmers
- submit-patric-annotation
- submit-patric-genbank