source: branches/profile/HELP_SOURCE/oldhelp/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.