| 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 sel_fil.hlp |
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| 8 | SUB phylo.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 Starting 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 ARB Parsimony cannot be used to completely reconstruct new trees. |
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| 19 | |
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| 20 | Existing trees can be optimized at different levels (depths) |
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| 21 | according to maximum parsimony criteria. |
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| 22 | |
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| 23 | New sequences (species) can be placed rapidly into an existing |
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| 24 | tree. This can be done without changing that tree or allowing |
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| 25 | optimization at different levels according to maximum parsimony |
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| 26 | criteria including the new information for calculation. |
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| 27 | |
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| 28 | The different ways to add species are explained in LINK{pa_quick.hlp}. |
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| 29 | Standard 'quick add' is available in this menu. To customize behavior |
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| 30 | or to optimize trees you have to start ARB parsimony in interactive mode. |
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| 31 | |
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| 32 | Filters for the in- or exclusion of alignment columns |
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| 33 | ('ARB_NT/SAI; ARB_NT/Tree/Dist Matrix) can be selected. |
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| 34 | |
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| 35 | After selecting one of the parsimony items in 'Tree/Add species to existing tree' |
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| 36 | the 'SET PARSIMONY OPTIONS' window appears: |
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| 37 | |
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| 38 | - Select the tree (to be modified) from the 'Tree:' subwindow. |
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| 39 | |
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| 40 | - Select an 'alignment' (see LINK{glossary.hlp}) from the |
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| 41 | 'alignment:' subwindow. |
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| 42 | |
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| 43 | - To select a filter display the 'Select Filter' window pressing |
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| 44 | the button after the 'Filter:' prompt (see LINK{sel_fil.hlp}). |
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| 45 | |
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| 46 | - Press the <GO> button to display the 'ARB_PARSIMONY' window. |
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| 47 | |
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| 48 | NOTES ARB Parsimony will modify the given tree. It might be a good idea to |
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| 49 | create a copy of your tree before you start doing so (see LINK{treeadm.hlp}). |
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| 50 | |
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| 51 | EXAMPLES None |
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| 52 | |
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| 53 | WARNINGS None |
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| 54 | |
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| 55 | BUGS No bugs known |
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