#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	glossary.hlp
UP	arb_edit4.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB	islandhopping.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		The integrated aligners

OCCURRENCE	ARB_EDIT4/Edit/Integrated Aligners

DESCRIPTION     Currently there are two integrated aligners:

                          1. Fast Aligner

                          2. Island Hopper (see Subtopic)

                The following adjustments and features should apply to both aligners.

                We did not test everything yet with island hopper, so some of them are broken.
                Please mail to LINK{devel@arb-home.de} if you find something.


SECTION         ADJUSTMENTS

                Align

                                Align current, marked or selected sequences.

                                If you type 'CTRL-A' in the main editor window
                                this option is set to align the current species and
                                the aligner gets called.

                Reference

                                The aligner needs a sequence as reference.
                                You can either

                                    * select a fixed species by name,
                                    * the consensus of the group containing the aligned species or
                                    * the next relative(s) found by the selected PT-Server.

                                If you choose 'Species by name', you may press the 'COPY' button
                                to copy the name of the 'Current Species' to the 'Reference' species.
                                Alternatively you may use CTRL-R while the focus is inside the sequence view
                                (Note: CTRL-R does not work, if LINK{viewdiff.hlp} is active).

                                If you choose 'Auto search by pt_server', the
                                aligner will use the next relative(s) as reference.

                                 * Please read section about 'Protein alignment with pt_server' below.

                                 * If the nearest relative has gaps where the sequence
                                   to align has bases, the aligner will use the 2nd nearest
                                   relative or if that one has gaps too, the 3rd nearest, etc.
                                   You can define the maximum number of relatives considered.

                                 * All used relatives and the number of base positions used from each relative,
                                   will be written into the field 'used_rels' (see also LINK{markbyref.hlp}).

                                If you enter '0' in 'Data from range only, plus', relative
                                search only uses data from the aligned range. If you enter
                                a value different from '0' the used range will be
                                expanded (positive values) or limited (negative values).
                                When the input field is empty, the complete sequence will be used.

                                Press 'More settings' to define how relative search works
                                in detail. See LINK{next_neighbours_common.hlp}

		Range

                                Align only a part of or the whole sequence.

				Several possibilities exist for aligning just a part of the sequence:
				- select 'Positions around cursor' and specify how many positions shall be 
				  taken into each direction from the cursor position (Example: If you align 
				  10 columns around position 100 then columns 90-110 will be aligned).
				- if you use 'Selected range' the column range of the selected block will 
				  be used.
				- if you select 'Multi-Range by SAI', the specified SAI will be interpreted as 
				  a list of ranges. A list of characters defines what is considered a range.
				  All ranges will be aligned.

				See also LINK{e4_modsai.hlp} for howto create suitable SAIs.

		Turn check

                                The aligner is able to detect sequences which
				were entered in the wrong direction. With this
				switch you can select, if you like the aligner
				to turn such sequences and if it should ask you.

				NOTE: In two cases turn checking isn't
				reasonable:

				If you align only a part of a sequence or if you
				do not search Reference via pt_server. In both
				cases turn checking will be disabled.

		Report

                                The aligner can generate reports for the aligned
				sequence and for the reference sequence. These
				reports can be viewed with EDIT4, if you choose
				File/Load Configuration/DEFAULT_CONFIGURATION

				The report for the reference sequence (AMI)
				contains a '>' for every position were the aligner
				needed an insert in the reference sequence.

				The report for the aligned sequence (ASC) contains
				the following characters:

                                    '-' for matching positions

                                    '+' for inserts (in aligned sequence and in reference sequence)

                                    '~' for matching, but not equal bases (A aligned to G, C aligned to T or U)

                                    '#' for mismatching positions

SECTION         Protein alignment with pt_server

                If you want to align protein sequences and use a PT-Server (to detect
                the next relative for each sequence),
                you need to

                     * have two alignments in your database (a protein alignment and a
                       corresponding DNA alignment). ARB has functions to synchronize these
                       alignments (see LINK{aaali.hlp}),
                     * build a pt_server based on the DNA-alignment,
                       select that pt_server in the aligner window and
                     * specify the name of the DNA-alignment in the 'Alignment' field.

NOTES	 	This aligner knows about and uses all extended base characters
		(ACGTUMRWSYKVHDN) for the alignment.
		In other words: M aligned to R costs no penalty.

		The config-manager icon handles the settings in the 'Integrated Aligners' window and those in
		its subwindows 'Parameters for Island Hopping' and 'Family search parameters'.

EXAMPLES	None

WARNINGS	None

BUGS		If you select the menu entry 'remove all aligner entries' ARB_EDIT4
		crashes in most cases.

		Workaround:

                        1. Close all groups containing species with aligner entries, so that no aligner entries are visible.
                        2. Remove all aligner entries
                        3. Reload configuration









