#       main topics:
UP      arb.hlp
UP      glossary.hlp

#       sub topics:
SUB     arb_gde.hlp
SUB     arb_db.hlp
SUB     arb_envar.hlp

# format described in ../help.readme


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!!!

        'arb_2_bin [-m] [-r] [-c][tree_xxx] database [newdatabase]'

                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
