source: branches/profile/HELP_SOURCE/oldhelp/ad_align.hlp

#Please insert up references in the next lines (line starts with keyword UP)
UP      arb.hlp
UP      glossary.hlp
UP      security.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB     insdel.hlp


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


TITLE           Alignment Administration

OCCURRENCE      ARB_NT/Sequence/Admin
                ARB_MERGE/Check alignments/MODIFY

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
                      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'.

                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