source: tags/arb_5.1/HELP_SOURCE/oldhelp/arb_pars.hlp

Last change on this file was 6142, checked in by westram, 15 years ago
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1#Please insert up references in the next lines (line starts with keyword UP)
2UP      arb.hlp
3UP      glossary.hlp
4
5#Please insert subtopic references  (line starts with keyword SUB)
6SUB     mode.hlp
7SUB     arb_pars_init.hlp
8SUB     ap_stack.hlp
9
10# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}
11
12#************* Title of helpfile !! and start of real helpfile ********
13
14TITLE           ARB Parsimony
15
16OCCURRENCE      ARB_NT/Tree/Add species to existing tree/Parsimony ...
17
18DESCRIPTION     The 'ARB_Parsimony' and 'ARB_NT' windows are similar. 'ARB_
19                Parsimony' contains a subset of 'ARB_NT' functions and in
20                addition some tolls for tree reconstruction and evaluation.
21
22        Clicking on the prompts in the horizontal menu bar in the upper part of
23        the window displays the corresponding submenus. The submenus are
24        also available using keyboard shortcuts by pressing the meta and
25        a letter key indicated in the main menu bar by underlining.
26
27        The buttons of the area between the main menu bar and the tree display
28        area (from left to right) ('called top area'):
29
30                First large button:     Displays the name of the current
31                                        tree.
32
33                Stack button:           Displays the number of stored tree
34                                        topologies
35
36                Jump button:            Displays partial tree within the tree
37                                        display area of the 'ARB_NT' window
38                                        containing the selected 'species' (see
39                                        LINK{glossary.hlp})
40
41                HELP button:            Displays this help information.
42
43                First small button:     Displays radial tree
44
45                Second small button:    Displays dendrogram
46
47                + and - buttons:        Define number of stored tree topologies.
48                                        Select version to be displayed.
49
50        The values after the 'Current Par' and 'Optimal Par' prompts indicate
51        current and optimal parsimony values for the displayed tree
52        while moving subtrees manually (see LINK{mode_move.hlp})
53
54        The program works on the selected tree, it does instantly change
55        the database.
56
57                FUNCTIONS:
58
59                        Tree/quick add marked species:
60
61                                Add all marked species to this tree.
62                                No local rearrangements are performed.
63                                If the species are already in the tree do
64                                nothing.
65
66                        Tree/quick add selected species:
67
68                                Add the selected species to this tree.
69                                To select a species open the 'Search & Query'
70                                window in ARB Ntree (ARB_NT/species/search);
71                                And select a species.
72                                or: start the editor, make the cursor global
73                                and select a sequence
74
75                        Tree/add marked species:
76
77                                Quick add plus local rearrangements.
78
79                        Tree/add selected species:
80
81                                Quick add sel. species plus local rearrangements.
82
83                        Tree/Optimization/Local
84
85                                Try to find a better tree moving all branches
86                                across one other branch. Does not change
87                                elements in folded subtrees.
88
89                        Tree/Optimization/Global
90
91                                Try to find a better tree by moving all branches,
92                                over some branches. Does not change
93                                elements in folded subtrees.
94                                Note: This may take a long time. You may stop the
95                                program any time and keep the current best tree.
96                                If you have to answer the question either to
97                                wait or to kill, answer wait.
98
99                        Tree/calculate branch lengths
100
101                                Does what it says
102
103                        etc.. see ARB Ntree
104
105
106
107
108NOTES           To create (small) parsimony trees use the phylip program
109
110
111EXAMPLES        None
112
113
114BUGS            None
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