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

#       sub topics:
SUB     nt_align_select.hlp
SUB     ad_align.hlp
SUB     pfold.hlp

# format described in ../help.readme


TITLE		What is an Alignment?

DESCRIPTION	Different alignments assigned to the same species (eg. sequences
		of different genes) can be stored in one database.
		The name of the currently accessible alignment (ali_*) is shown
		in the 3rd broad rectangular button in the top area of the
 		ARB_NT window.

		The sequences themselves are not stored in the 'ali_*' field of
		a species, but in the subfield 'data' of 'ali_*'
		'ali_*' is a container field: it holds no data
		except other data fields (like a directory in a file system).

NOTE            There is a special alignment called 'ali_genom' which is used
                for full genome databases.
                It's called an alignment because it fits into our database structure,
                but it should NOT contain any gaps.