| 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 subtopic.hlp |
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| 7 | |
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| 8 | # format described in ../help.readme |
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| 9 | |
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| 10 | |
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| 11 | TITLE Selected species |
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| 12 | |
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| 13 | OCCURRENCE ARB wide |
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| 14 | |
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| 15 | DESCRIPTION One individual species can be "selected" at a time. |
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| 16 | We refer to it when talking about the "selected species". |
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| 17 | |
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| 18 | Selecting a species has several effects: |
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| 19 | |
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| 20 | * the database fields of the selected species get displayed in the LINK{sp_info.hlp} window, |
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| 21 | * the ID ('name') of the selected species will be displayed on the species info button |
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| 22 | in the upper right area of the ARB main window, |
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| 23 | * the tree display of ARB draws a box as indicator next to the selected species, |
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| 24 | * ARB_EDIT4 will jump to the selected species (see LINK{e4_get_species.hlp} for details), |
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| 25 | - this allows you e.g. to align the selected species (see LINK{faligner.hlp}) |
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| 26 | * ARB_SECEDIT will display the selected species (see LINK{arb_secedit.hlp}) |
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| 27 | * ARB_PARS can insert the selected species into an existing tree (see LINK{pa_quick.hlp}) |
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| 28 | * it can be used for filter generation (see LINK{sel_fil.hlp}) |
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| 29 | * LINK{input_mask.hlp} will normally display information from the selected species |
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| 30 | |
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| 31 | There are several ways to select a species: |
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| 32 | |
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| 33 | * in ARB main window and ARB_PARSIMONY: |
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| 34 | * click on a species in the tree display (while in LINK{mode_select.hlp}) |
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| 35 | * search for species and select a species from the result list (see LINK{sp_search.hlp}) |
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| 36 | * select a LINK{probematch.hlp} |
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| 37 | * use the hotkeys described in LINK{nt_keys.hlp} (in section "Selecting species") |
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| 38 | |
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| 39 | * in ARB_EDIT4: |
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| 40 | * place the cursor into a species by clicking into the displayed sequence data |
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| 41 | |
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| 42 | * in ARB_DIST: |
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| 43 | * click on a species name in matrix display |
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| 44 | * select a detected cluster (see LINK{di_clusters.hlp}) while 'Select representative' is checked |
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| 45 | |
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| 46 | * in ARB_MERGE: |
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| 47 | * search for species and select a species from any result list (see LINK{mg_species.hlp}) |
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| 48 | * Please note that ARB_MERGE has one selected species for EACH involved database! |
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| 49 | |
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| 50 | SECTION Global sequence position |
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| 51 | |
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| 52 | Selecting a species in ARB_EDIT4 (by clicking into the sequence data), will also select a |
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| 53 | global cursor position. This cursor position is displayed in the ARB_EDIT4 |
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| 54 | top area (see LINK{e4.hlp}) and will be used |
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| 55 | |
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| 56 | * as insert/delete position by LINK{insdel.hlp} and |
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| 57 | * as start of ORF by LINK{translate_dna_2_pro.hlp}. |
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| 58 | |
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| 59 | NOTES |
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| 60 | |
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| 61 | * ARB offers the possibility to select taxonomic groups (see LINK{nt_keys.hlp} |
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| 62 | and LINK{group_search.hlp}). Whenever a group gets selected, the selection is |
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| 63 | removed from the selected species and vice versa. |
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| 64 | * "Marking" species is a different concept, which is described in LINK{mark.hlp}. |
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| 65 | * Please note LINK{species_configs.hlp} are not related to the 'selected species'. |
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| 66 | |
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