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UP	arb.hlp
UP	glossary.hlp
UP	security.hlp

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#************* Title of helpfile !! and start of real helpfile ********


TITLE		Alignment Administration

OCCURRENCE	ARB_NT/Sequence/Admin

DESCRIPTION  This module allows handling and modification of 'alignments'
             (see LINK{glossary.hlp}).

		Select an alignment from the 'Alignments' subwindow

		Define the type of sequences (DNA, RNA, protein):

			Press the <Type of Sequences> button and choose from the
			displayed menu.

		Set protection:

			Press the <Default Write Protection> button and choose
			from the displayed menu.

		Press the respective buttons to perform further functions:

                      DELETE:	  Delete an alignment and its sequence data
                      RENAME:	  Rename an alignment
                      CREATE:	  Create a new alignment (no data)
                      COPY:	  Copy an alignment
                      SEQ REMARK: Add a remark field to the sequence of the selected SAI
                      CHECK LEN:  Find the longest sequence and set the
                                  'Maximum Seq. Length' displayed in the
                                  corresponding subwindow [*]
                      FORMAT:     Append '.' to sequences up to 'Maximum Seq.
                                  Length'. [*]

                Auto format: Whether to ask, format or skip w/o asking
                             whenever an unformatted alignment is detected.

NOTES		Some functions require setting a protection level equal to or
		higher than that of the 'alignment'.

		Asterisks indicate functions which are not available with the
		'ALIGNMENT CONTROL' functions of the 'MERGE TWO DATABASES' tool.

                There is one special alignment called "ali_genom" used for full
                genome sequences. You can't format that alignment because it is
                necessary to ensure that it's alignment positions match those
                used in the gene entries. For the same reason you should never
                ever put any gap into that alignment.

EXAMPLES	None

WARNINGS	Be careful when deleting or changing the name of an alignment
		while other programs are using it (eg. parsimony programs ..)

BUGS		No bugs known
