#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    subtopic.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           Split sequences

OCCURRENCE      ARB_NT/Sequence/Split sequences

DESCRIPTION     Allows to split an alignment into multiple alignments.

                One usecase of this function is to
                 1. split an alignment into multiple partial alignments (parts)
                 2. operate on single parts only (e.g. using an aligner)
                 3. join the (modified) parts into the original alignment
                    using LINK{concatenate.hlp}.

                Insert the "Target alignment prefix".
                This string will be appended by digits and
                then gets used as names of the generated partial alignments.

                Insert a list of positions (comma-separated).
                The source alignment will be split before each of the
                given positions and the splitted sequence parts will
                be written into separate target alignments.

                    The easiest way to select positions to split is to
                    * highlight a block in the arb sequence editor and
                    * then click "Use editor range".

                Choose whether all or only marked sequences should get splitted.

                You may choose to overwrite existing alignments.
                This will completely delete these alignments and the stored data
                for any species or SAI w/o further confirmation.

NOTES           When reducing the number of split positions while using
                the option to overwrite existing alignments,
                unused/unwanted alignments may remain.
                Consider using DELETE from LINK{ad_align.hlp} manually in that case.

                The comment attached to each alignment does contain information about
                source, time and parts of each performed split, i.e. you may use the comment
                to decide whether alignments were generated in one split or are relicts
                from earlier splits.

SECTION         SAI handling

                SAI data is handled more diversely:
                - when data is considered to be alignment relative, arb splits its contents
                  into single partial alignments.
                - otherwise the content gets prefixed by the tag '[splitted]'.
                - some entries like 'FREQUENCIES' are not transferred. A placeholding comment
                  is inserted into the target alignment instead.

                SAIs like 'HELIX' are most likely functionally broken after splitting the alignment.

EXAMPLES        None

WARNINGS        None

BUGS            No bugs known
