| 1 | # main topics: |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | |
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| 5 | # sub topics: |
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| 6 | SUB mode.hlp |
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| 7 | SUB arb_pars_init.hlp |
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| 8 | SUB ap_stack.hlp |
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| 9 | |
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| 10 | # format described in ../help.readme |
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| 11 | |
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| 12 | |
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| 13 | |
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| 14 | TITLE ARB Parsimony |
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| 15 | |
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| 16 | OCCURRENCE ARB/Tree/Add species to existing tree/Parsimony ... |
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| 17 | |
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| 18 | DESCRIPTION The 'ARB_Parsimony' and the ARB main window are similar. |
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| 19 | 'ARB_Parsimony' replicates a smaller subset of the normal ARB's functions, |
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| 20 | and additionally adds several tools for tree reconstruction and evaluation. |
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| 21 | |
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| 22 | Clicking on the prompts in the horizontal menu bar in the upper part of |
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| 23 | the window displays the corresponding submenus. The submenus are |
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| 24 | also available using keyboard shortcuts by pressing the meta and |
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| 25 | a letter key indicated in the main menu bar by underlining. |
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| 26 | |
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| 27 | The elements in the area between the main menu bar and the tree display |
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| 28 | area ('top area') from left to right: |
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| 29 | |
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| 30 | * Tree button: Displays the name of the current tree. |
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| 31 | * Stack button: Displays the number of currently stored tree topologies (see LINK{ap_stack.hlp}). |
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| 32 | * Current parsimony value: Displays the parsimony value of the |
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| 33 | current topology (see LINK{pa_value.hlp}). |
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| 34 | * Jump button: Centers the currently LINK{selected.hlp}. |
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| 35 | * HELP button: Displays this help information. |
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| 36 | |
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| 37 | Second row |
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| 38 | |
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| 39 | * Radial tree display |
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| 40 | * Dendrogram tree display |
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| 41 | * RESTORE: restores previously stored topology |
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| 42 | * STORE: stores the current topology for later restore |
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| 43 | * Optimal parsimony value: Displays the best so far encountered parsimony value (see LINK{pa_reset.hlp}). |
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| 44 | |
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| 45 | Main functions: |
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| 46 | |
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| 47 | * quick adding species (see LINK{pa_quick.hlp}) |
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| 48 | * add species with local optimization (see LINK{pa_add.hlp}) |
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| 49 | * topology optimization (see LINK{pa_optimizer.hlp}) |
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| 50 | |
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| 51 | |
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| 52 | NOTES ARB_PARSIMONY is not designed to CREATE trees from scratch. |
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| 53 | To do this you have to create a base tree containing at least 2 species |
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| 54 | using some other program (e.g. LINK{dist.hlp}). |
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| 55 | |
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| 56 | WARNINGS ARB_PARSIMONY works on the selected tree, it does instantly change the database. |
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| 57 | |
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| 58 | EXAMPLES None |
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| 59 | |
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| 60 | BUGS None |
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