source: trunk/HELP_SOURCE/source/nt_tree_settings_bootstrap.hlp

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UP      arb.hlp
UP      glossary.hlp
UP      nt_tree_settings.hlp

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SUB    multifurcate.hlp
SUB    mode_length.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           Bootstrap display settings

OCCURRENCE      ARB_NT/Properties/Tree options/Bootstrap settings

DESCRIPTION     The following bootstrap related display settings are available:

                - 'Show bootstraps' completely toggles whether bootstrap values etc.
                  will be displayed in the tree view.

                - 'Hide bootstrap below' and 'Hide bootstrap above' allow to configure
                  which range of bootstrap values is shown in the tree.

                  Generally, branches with less than 50% cannot be regarded as supported
                  (see also section about 'Bootstrap circle size' below).

                  If a bootstrap value is hidden => no circle/ellipse will be displayed.

                  Please note that bootstrap values at branches with zero length will never be
                  displayed in ARB.
                  Such branches occur as parts of multifurcations and are regarded as "non-present".
                  Nevertheless such bootstrap values are NOT removed from trees (i.e. they'll appear again when
                  you export the tree).

                - 'Bootstrap style' allows to select one of the following display styles:
                   * 'percent%' (<1% .. 100%)
                   * 'percent' (<1 .. 100)
                   * 'float' (<0.01 .. 1.00)

                - 'Show bootstrap circles' toggles the display of bootstrap circles (only
                  available if the tree contains bootstrap values).

                - 'Greylevel of circles' allows to configure the shading level of bootstrap
                  circles/disks.

                - If 'Use ellipse' is active, ellipses instead of circles are drawn in
                  dendrogram tree.

                - 'Bootstrap circle zoom factor' allows to increase/reduce the size
                  of the bootstrap circles/ellipse

                - 'Bootstrap radius limit' allows to limit the max. bootstrap circle/ellipse size.
                  If a bootstrap exceeds this limit its circle/ellipse will be drawn in a different
                  color.

NOTES           These settings will be managed together with other tree settings (use config
                icon in 'Tree settings' window)

SECTION         Bootstrap circle size

                The radius of the bootstrap circle depends on the bootstrap value itself,
                on the length of the branch from the node towards the tree root and on the
                configured zoom factor/limit.

                For a zoom factor of 1, a bootstrap value of ~44% will show a circle/ellipse
                which completely contains the whole branch.

                Such a bootstrap value indicates a certain fuzziness and the
                associated bootstrap circle attempts to graphically visualize
                that fuzziness.

                Branches covered or overlapped by circles can be
                considered more or less unstable.

                For increasing bootstrap values the radius goes towards zero; for smaller
                bootstrap values the radius will get infinite - that is why ARB uses
                a 'Bootstrap radius limit'.

                The formula used to calculate the (unlimited) bootstrap circle radius is

                        (1/sqrt(bootstrap/100) - 1) * 2*branchlength


EXAMPLES        None

WARNINGS        None

BUGS            No bugs known