| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | UP nt_tree_settings.hlp |
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| 5 | |
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| 6 | #Please insert subtopic references (line starts with keyword SUB) |
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| 7 | #SUB subtopic.hlp |
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| 8 | |
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| 9 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 10 | |
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| 11 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 12 | TITLE Bootstrap display settings |
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| 13 | |
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| 14 | OCCURRENCE ARB_NT/Properties/Tree options/Bootstrap settings |
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| 15 | |
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| 16 | DESCRIPTION The following bootstrap related display settings are available: |
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| 17 | |
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| 18 | - 'Show bootstraps' completely toggles whether bootstrap values etc. |
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| 19 | will be displayed in the tree view. |
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| 20 | |
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| 21 | - 'Hide bootstrap below' and 'Hide bootstrap above' allow to configure |
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| 22 | which range of bootstrap values is shown in the tree. |
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| 23 | |
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| 24 | Generally, branches with less than 50% cannot be regarded as supported |
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| 25 | (see also section about 'Bootstrap circle size' below). |
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| 26 | |
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| 27 | If a bootstrap value is hidden => no circle/ellipse will be displayed. |
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| 28 | |
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| 29 | - 'Bootstrap style' allows to select one of the following display styles: |
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| 30 | * 'percent%' (<1% .. 100%) |
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| 31 | * 'percent' (<1 .. 100) |
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| 32 | * 'float' (<0.01 .. 1.00) |
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| 33 | |
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| 34 | - 'Show bootstrap circles' toggles the display of bootstrap circles (only |
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| 35 | available if the tree contains bootstrap values). |
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| 36 | |
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| 37 | - 'Greylevel of circles' allows to configure the shading level of bootstrap |
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| 38 | circles/disks. |
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| 39 | |
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| 40 | - If 'Use ellipse' is active, ellipses instead of circles are drawn in |
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| 41 | dendrogram tree. |
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| 42 | |
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| 43 | - 'Bootstrap circle zoom factor' allows to increase/reduce the size |
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| 44 | of the bootstrap circles/ellipse |
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| 45 | |
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| 46 | - 'Bootstrap radius limit' allows to limit the max. bootstrap circle/ellipse size. |
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| 47 | If a bootstrap exceeds this limit its circle/ellipse will be drawn in a different |
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| 48 | color. |
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| 49 | |
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| 50 | NOTES These settings will be managed together with other tree settings (use config |
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| 51 | icon in 'Tree settings' window) |
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| 52 | |
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| 53 | SECTION Bootstrap circle size |
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| 54 | |
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| 55 | The radius of the bootstrap circle depends on the bootstrap value itself, |
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| 56 | on the length of the branch from the node towards the tree root and on the |
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| 57 | configured zoom factor/limit. |
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| 58 | |
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| 59 | For a zoom factor of 1, a bootstrap value of ~44% will show a circle/ellipse |
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| 60 | which completely contains the whole branch. |
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| 61 | |
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| 62 | Such a bootstrap value indicates a certain fuzziness and the |
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| 63 | associated bootstrap circle attempts to graphically visualize |
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| 64 | that fuzziness. |
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| 65 | |
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| 66 | Branches covered or overlapped by circles can be |
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| 67 | considered more or less unstable. |
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| 68 | |
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| 69 | For increasing bootstrap values the radius goes towards zero; for smaller |
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| 70 | bootstrap values the radius will get infinite - that is why ARB uses |
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| 71 | a 'Bootstrap radius limit'. |
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| 72 | |
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| 73 | The formula used to calculate the (unlimited) bootstrap circle radius is |
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| 74 | |
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| 75 | (1/sqrt(bootstrap/100) - 1) * 2*branchlength |
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| 76 | |
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| 77 | |
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| 78 | EXAMPLES None |
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| 79 | |
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| 80 | WARNINGS None |
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| 81 | |
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| 82 | BUGS No bugs known |
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