| 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 arb_pars.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 sub.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 Tree optimization |
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| 13 | |
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| 14 | OCCURRENCE ARB_PARSIMONY/Tree/Tree Optimization |
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| 15 | |
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| 16 | DESCRIPTION This subwindow allows you to configure and access |
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| 17 | LINK{pa_locopti.hlp}, LINK{pa_globopti.hlp} and LINK{pa_mixtree.hlp}. |
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| 18 | |
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| 19 | First you can select whether these functions are applied to the whole tree or |
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| 20 | whether they only operate on subtrees containing marked species and/or they |
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| 21 | only operate on visible (i.e. unfolded) parts of the tree. |
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| 22 | |
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| 23 | Note: |
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| 24 | |
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| 25 | The default behavior until arb-7.0 was to operate on marked and visible parts |
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| 26 | only. Due to several, now fixed bugs it did not strictly restrict to these parts |
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| 27 | while optimizing. |
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| 28 | |
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| 29 | Then you may trigger the wanted optimization/randomization using the following buttons: |
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| 30 | |
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| 31 | * 'Recursive NNI' will trigger LINK{pa_locopti.hlp} |
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| 32 | * 'Heuristic optimizer' will trigger LINK{pa_globopti.hlp} |
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| 33 | * 'Randomize tree' will trigger LINK{pa_mixtree.hlp} |
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| 34 | |
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| 35 | For the 'Heuristic optimizer' click 'Settings' to change LINK{kernlin.hlp}. |
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| 36 | |
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| 37 | NOTES When only optimizing subtrees with marked species, only branches that are drawn in |
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| 38 | 'Marked' or 'Some marked' color will be modified. |
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| 39 | |
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| 40 | The tree optimizations may as well be called using the 3 tree-modes LINK{mode_nni.hlp}, |
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| 41 | LINK{mode_kernlin.hlp} and LINK{mode_optimize.hlp}. Opposed to using the buttons in |
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| 42 | the 'Tree optimization' window, these modes normally operate on the clicked subtree only. |
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| 43 | |
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| 44 | After any optimization/randomization the tree will be 'beautified' (see |
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| 45 | LINK{resorttree.hlp}) and branchlengths will be re-calculated (see LINK{pa_branchlengths.hlp}). |
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| 46 | |
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| 47 | Saving the current settings as configuration will save the properties from this window |
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| 48 | and from the LINK{kernlin.hlp} window. |
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| 49 | |
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| 50 | EXAMPLES None |
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| 51 | |
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| 52 | WARNINGS None |
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| 53 | |
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| 54 | BUGS No bugs known |
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