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#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!!!
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 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
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