source: trunk/HELP_SOURCE/source/dist.hlp

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

#Please insert subtopic references  (line starts with keyword SUB)
SUB     user_matrix.hlp
SUB     savedef.hlp
SUB     props_frame.hlp
SUB     sel_fil.hlp
SUB     awt_csp.hlp
SUB     bootstrap.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           Neighbour joining

OCCURRENCE      ARB_NT/Tree/Build tree from sequence data/Distance matrix methods/Distance matrix + ARB NJ

DESCRIPTION     Reconstructs a tree for all or marked species by first
                calculating binary distances and subsequently applying the
                neighbour joining method.

                The tree topology is stored in the database and can be displayed
                within the tree display area of the 'ARB_NT' window.

                1. Mark all interesting species.

                2. Select all or marked species from the 'Select Species' menu
                   of the 'NEIGHBOUR JOINING' window.

                3. Select Alignment from the 'Select Alignment' subwindow of
                   the 'NEIGHBOUR JOINING' window.

                4. Display the 'Select Filter' window by pressing the button
                   after the 'Filter' prompt and define an alignment-associated
                   mask which defines alignment positions to include for treeing.

                5. Define Weights: @@@ not implemented

                6. Select rate matrix (only implemented for some corrections; see LINK{user_matrix.hlp})

                7. Type characters for the exclusion of alignment postions to
                   the 'Exclude Column' subwindow. The positions are
                   excluded from the calculation of binary distance values
                   if one of the specified characters is present in one or
                   both sequences. The described function acts as a second
                   filter and affects only the particular sequence
                   pairs, not the whole alignment.

                   Possible settings are "" (empty), "." and ".-".

                      - "" treats dots as separate gap-type (i.e. '.' vs. '-' counted as mutation)
                      - "." does not count dots (over-rates gaps running over multiple columns)
                      - ".-" does not count gaps (ignores insertions and deletions)

                   Note: This setting is ignored when using a LINK{user_matrix.hlp} or
                         if Kimura correction is selected.

                8. Select the type of distance correction from the 'Distance
                   Correction' submenu. You can use the program to detect
                   the best correction for you by pressing the AUTODETECT
                   button.

                   none:

                        Differences/Sequence length. May be a good
                        choice for short sequences (length < 300).

                   similarity:

                        1.0 - Differences/Sequence_Length

                   jukes-cantor:

                        Accounts for multiple base changes, assumes
                        equal base frequencies.
                        Good choice for medium sized sequences
                        ( 300 - 1000/2000 sequence length )

                   felsenstein:

                        Similar to jukes-cantor transformation. Allows
                        unequal base frequencies.
                        ( length > 1000/2000 )

                   olsen:

                        As Felsenstein, except the base frequencies are
                        calculated for each pair of sequences.

                   from selected tree:

                        This is NOT a distance correction! By selecting 'from selected tree'
                        distances are not calculated using sequence data.
                        Instead they are extracted from the
                        tree currently selected in the 'Trees in Database' selection list.

                        The distance between two species is defined as the sum of the lengths
                        of all branches that connect these two species.

                        Please note that this is an experimental feature. The distances between two species
                        are not directly based on the sequence differences between these two species.
                        Instead they reflect the evolutionary distance assumed by the tree reconstruction
                        algorithm used to build the tree.

                        The distances extracted from a tree are expected to be (slightly) bigger than
                        the distances directly calculated from the sequences.
                        This seems reasonable, because it is very unlikely, that evolution always took the
                        shortest possible way (which is represented by the direct sequence distance).
                        This effect increases for more distant (unrelated) species, reflecting the
                        indirections evolution most likely made.

                   Please note:

                          the other correcting functions are in an experimental state.
                          Wait for new release.!!!

                9. Select a name for the tree from the 'Trees in Database'
                   subwindow or type a new tree name.
                   The tree name has to be 'tree_*'.
                   An existing tree with that name will be deleted.

                10. Press the 'CALCULATE TREE' button

                11. Now you may display the new tree in the ARB_NT main window
                        by selecting its name from the <Tree/Select> subwindow.
                        If its name is already selected, you will not need to
                        reselect it.

                The distance matrix can be written to an ascii file:

                        Press the <SAVE MATRIX> button to display the 'SAVE
                        MATRIX' window. Select a file from the 'Directories
                        and Files' subwindow or type a file name to the 'FILE
                        NAME' subwindow. Press the <SAVE> button.
                        The suffix displayed in the 'SUFFIX' subwindow is added
                        to the typed file name and defines the selection of
                        files listed in the 'Directories and Files' subwindow.

SECTION         Calculate compressed matrix

                You may select a tree to calculate a compressed matrix. A 
                compressed matrix contains columns for all folded groups 
                visible in the displayed tree (i.e. not for unfolded groups
                and not for folded groups inside other folded groups).
                
                Species inside such groups are NOT listed as single entries.
                
                The distance shown for each group is the arithmetic average of 
                of the distances of all contained species.

SECTION         Automatic calculation

                There are two toggles in the ARB_DIST main window allowing to
                trigger instant recalculation:

                - 'Auto recalculate' will force recalculation of the matrix
                - 'Auto calculate tree' will force calculation of the tree

                If 'Auto calculate tree' is checked, the tree will be calculated
                whenever the matrix has been updated.

                If 'Auto recalculate' is checked, the matrix will be recalculated
                whenever any input changes, e.g. if

                - the filter is changed (or its underlaying SAI changes),
                - the excluded columns change,
                - the user defined matrix changes,
                - the correction is changed,
                - the sequence data changes or species marks change or
                - the tree selected for compression or sorting changes or a different
                  tree is selected.

                As you might have guessed, this is only useful for smaller sets of sequences.

                Some suggestions:

                     You might for example display the resulting NJ tree in one window and
                     play with distance parameter to instantly see their effect on the tree.

                     Or you may unmark unwanted species/subtrees in the tree display.

                     Or you might align sequences to see the effect on the resulting topology.


NOTES           Computing time can be estimated using the following formula:

                        time = (Sequence_Length * Nr.of.Spec * Nr.of.Spec)/
                                Computer Power

                                Example: Sparc 10, 74 Sequences, length 8000 characters
                                         -> 10 Seconds


WARNINGS        Don't try to build a tree with the 'similarity' distance
                correction selected.

                Distance values calculated without distance correction are strictly inside range [0.0 .. 1.0].
                Same is true for 'similarity' distance "correction".
                With distance corrections, the range does vary depending on the correction method.

BUGS            None