source: trunk/HELP_SOURCE/source/alignment.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     nt_align_select.hlp
SUB     ad_align.hlp
SUB     pfold.hlp

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

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