Tree Pattern Matching Daemon command line documentation

NAME:

- Reconciliation Database Daemon v1.0 -

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SYNOPSIS:

reconciliationdatabasedaemon [command args]

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MAIN OPTIONS:

    -standard database_id species_tree_file gene_tree_file

            The identifier of the database, the species tree file, the file containing all gene trees in NHX format.

    -quiet

        Activate this option to turn off the default verbose mode

    -config config_file

    	Configuration file for this occurrence of the server, used to define example patterns available from the web interface, related to the database.

    -port port

            The logical port that must be open, and will serve as communication network link for the web interface (default 1666).

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CONFIDENTIAL OPTIONS:

    -database database_id species_tree_file gene_tree_directory gene_tree_file

            The identifier of the database, the species tree file, the directory containing all gene tree files, and the tree file name eventually containing 'INPUT' marker for directory name.

    -directory database_id species_tree_file gene_tree_directory type

    	Alternate version of database option: one simple directory full of gene trees. Arguments are: the identifier of the database, the species tree file, the directory containing all gene tree files, and the type of the database (NR, DL or DTL).

    -directoryDico database_id species_tree_file species_dictionary gene_tree_directory type

    	Alternate version of database option: one simple directory full of gene trees, and using a species dictionary. Arguments are: the identifier of the database, the species tree file , the species dictionary, the directory containing all gene tree files, and the type of the database (NR, DL or DTL).

    -fileDico database_id species_tree_file species_dictionary gene_tree_file type [invert]

    	Alternate version of database option: one simple file full of gene trees, and using a species dictionary. Arguments are: the identifier of the database, the species tree file , the species dictionary, the directory containing all gene tree files, and the type of the database (NR, DL or DTL). Add invert keyword if the species identifier is at the begining of sequence names in phylogenetic trees.

    -genomicus database_id species_tree_file gene_tree_file

    	 Alternate version to load a Genomicus tree file and the corresponding species tree file

    -instantGenomicusPatternSearch species_tree_file gene_tree_file pattern outputCSV

    	 Alternate version to load a Genomicus tree file and the corresponding species tree file, then search the pattern locally, produce the output CSV and close de program.