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 | |
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5 | #Please insert subtopic references (line starts with keyword SUB) |
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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 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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11 | |
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12 | #************* Title of helpfile !! and start of real helpfile ******** |
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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_NT/Tree/Add species to existing tree/Parsimony ... |
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17 | |
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18 | DESCRIPTION The 'ARB_Parsimony' and 'ARB_NT' windows are similar. 'ARB_ |
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19 | Parsimony' contains a subset of 'ARB_NT' functions and in |
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20 | addition some tolls 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 buttons of the area between the main menu bar and the tree display |
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28 | area (from left to right) ('called top area'): |
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29 | |
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30 | First large button: Displays the name of the current |
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31 | tree. |
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32 | |
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33 | Stack button: Displays the number of stored tree |
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34 | topologies |
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35 | |
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36 | Jump button: Displays partial tree within the tree |
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37 | display area of the 'ARB_NT' window |
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38 | containing the selected 'species' (see |
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39 | LINK{glossary.hlp}) |
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40 | |
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41 | HELP button: Displays this help information. |
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42 | |
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43 | First small button: Displays radial tree |
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44 | |
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45 | Second small button: Displays dendrogram |
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46 | |
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47 | + and - buttons: Define number of stored tree topologies. |
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48 | Select version to be displayed. |
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49 | |
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50 | The values after the 'Current Par' and 'Optimal Par' prompts indicate |
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51 | current and optimal parsimony values for the displayed tree |
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52 | while moving subtrees manually (see LINK{mode_move.hlp}) |
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53 | |
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54 | The program works on the selected tree, it does instantly change |
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55 | the database. |
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56 | |
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57 | FUNCTIONS: |
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58 | |
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59 | Tree/quick add marked species: |
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60 | |
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61 | Add all marked species to this tree. |
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62 | No local rearrangements are performed. |
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63 | If the species are already in the tree do |
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64 | nothing. |
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65 | |
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66 | Tree/quick add selected species: |
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67 | |
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68 | Add the selected species to this tree. |
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69 | To select a species open the 'Search & Query' |
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70 | window in ARB Ntree (ARB_NT/species/search); |
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71 | And select a species. |
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72 | or: start the editor, make the cursor global |
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73 | and select a sequence |
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74 | |
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75 | Tree/add marked species: |
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76 | |
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77 | Quick add plus local rearrangements. |
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78 | |
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79 | Tree/add selected species: |
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80 | |
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81 | Quick add sel. species plus local rearrangements. |
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82 | |
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83 | Tree/Optimization/Local |
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84 | |
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85 | Try to find a better tree moving all branches |
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86 | across one other branch. Does not change |
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87 | elements in folded subtrees. |
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88 | |
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89 | Tree/Optimization/Global |
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90 | |
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91 | Try to find a better tree by moving all branches, |
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92 | over some branches. Does not change |
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93 | elements in folded subtrees. |
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94 | Note: This may take a long time. You may stop the |
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95 | program any time and keep the current best tree. |
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96 | If you have to answer the question either to |
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97 | wait or to kill, answer wait. |
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98 | |
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99 | Tree/calculate branch lengths |
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100 | |
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101 | Does what it says |
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102 | |
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103 | etc.. see ARB Ntree |
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104 | |
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105 | |
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106 | |
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107 | |
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108 | NOTES To create (small) parsimony trees use the phylip program |
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109 | |
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110 | |
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111 | EXAMPLES None |
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112 | |
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113 | |
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114 | BUGS None |
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