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Last update on 04. Mar 2022 .
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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)

 

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