source: branches/stable/HELP_SOURCE/oldhelp/arb_commands.hlp

#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB     arb_gde.hlp
SUB     arb_db.hlp
SUB     arb_envar.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real strunk ********
TITLE           ARB: Basic ARB-Shell Commands

OCCURRENCE      shell

SECTION         COMMANDS

        'arb [filename]'

                Starts the main program ARB_NT which also includes the database
                server.

                The database server is memory based. That means:

                        - All changes are only temporary until the
                          database is saved.
                        - The database is a single file which can be copied,
                          deleted, renamed ...

                The database file should have the suffix '.arb'.


        'arb_clean'

                Stops all your ARB processes and removes all temporary files in
                the /tmp directory.
                It does not kill non-arb processes. That means if you start
                programs via the GDE interface you have to stop them yourself:
                (phylip, desoete, ...)

                        enter 'ps -ux'   or 'ps -f'
                        search the process-id PID and kill it with
                        'kill -9 PID'

        'arb_panic'

                Sends a signal (HANGUP) to ARB_NT to force saving the
                database in ASCII mode.
                Because arb_panic bypasses any running operation of ARB_NT,

                THE SAVED DATABASE MAY CONTAIN INCONSISTENT DATA.

                It interactively asked for file name and whether it should
                kill arb after saving.

        'arb_2_ascii filename [dest_filename]'

                Converts any ARB database to ASCII format.

                Also tries to recover corrupt files (if dest_filename is skipped).
                Backup first!!!

        Žarb_2_bin [-m] [-r] [-c][tree_xxx] database [newdatabase]Ž

                Purpose: Converts a database to binary format

                Options:
                         -m            create map file too
                         -r            try to repair destroyed database
                         -c[tree_xxx]  optimize database compression using tree_xxx or largest tree

NOTES           It is very useful to start a performance meter to see
                whether there are running background jobs (fastdnaml, phylip...)

                All arb_... commands show some basic usage info if you call
                them with parameter '--help'

                        i.e.    arb_ntree --help

WARNINGS        Don't destroy an existing arb file with arb_panic.

BUGS            No bugs known