| 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 arb.pdf |
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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 trees.hlp |
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| 7 | SUB helix.hlp |
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| 8 | SUB props_nds.hlp |
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| 9 | SUB pt_server.hlp |
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| 10 | SUB extended.hlp |
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| 11 | SUB species.hlp |
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| 12 | SUB selected.hlp |
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| 13 | |
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| 14 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 15 | |
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| 16 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 17 | TITLE Glossary |
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| 18 | |
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| 19 | SECTION What do we mean if we talk about ... |
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| 20 | |
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| 21 | ALIGNMENT |
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| 22 | |
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| 23 | Subdatabase containing homologous sequences (different |
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| 24 | 'alignments' can be stored along with the species information). |
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| 25 | See LINK{alignment.hlp} for more information. |
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| 26 | |
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| 27 | ACI |
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| 28 | |
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| 29 | ARB Command Interpreter. ACI is a simple programing language |
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| 30 | for calculating special species information (eg. G+C Content..) |
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| 31 | See LINK{aci.hlp}. |
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| 32 | |
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| 33 | EDGE |
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| 34 | |
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| 35 | Branch within a tree defined by nodes |
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| 36 | |
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| 37 | FIELD |
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| 38 | |
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| 39 | Container for 'species' associated information |
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| 40 | |
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| 41 | MARKED SPECIES |
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| 42 | |
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| 43 | Marking of 'species' defines the datasubset which is analyzed |
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| 44 | by the ARB tools. |
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| 45 | See LINK{mark.hlp}. |
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| 46 | |
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| 47 | NAMES |
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| 48 | |
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| 49 | There are two kinds of name fields (for species, genes, etc.). |
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| 50 | |
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| 51 | - name |
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| 52 | |
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| 53 | Identifier for 'species' entries. |
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| 54 | Should be generated automatically using |
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| 55 | the NAMESERVER (see LINK{sp_IDs.hlp}). |
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| 56 | |
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| 57 | - full_name |
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| 58 | |
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| 59 | User defined full name of the species,... |
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| 60 | |
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| 61 | NDS |
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| 62 | |
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| 63 | Node Display Setup: defines information which is displayed at |
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| 64 | tree nodes. |
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| 65 | |
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| 66 | NODE |
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| 67 | |
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| 68 | Internal: connects branches of a tree |
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| 69 | Terminal: free end of branches representing 'species' |
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| 70 | |
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| 71 | PT_SERVER |
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| 72 | |
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| 73 | Server using a special form of the ARB database for rapid |
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| 74 | similarity searching (automated alignment, probe design/check) |
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| 75 | |
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| 76 | SAI |
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| 77 | |
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| 78 | Sequence Associated Information (see LINK{ad_extended.hlp}) |
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| 79 | |
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| 80 | SELECTED SPECIES |
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| 81 | |
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| 82 | See LINK{selected.hlp}. |
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| 83 | |
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| 84 | SPECIES |
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| 85 | |
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| 86 | Database entry containing a sequence and associated information. |
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| 87 | Not necessarily consistent with a taxonomic species |
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| 88 | |
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| 89 | SRT |
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| 90 | |
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| 91 | Search and Replace Tool allows to search substrings in a string |
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| 92 | and replace them by another substring (see LINK{srt.hlp}). |
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| 93 | |
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| 94 | ZOMBIES |
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| 95 | |
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| 96 | Zombies are references to former species in a tree, i.e. to species |
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| 97 | that were in the database when the tree has been calculated, but |
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| 98 | have meanwhile been deleted (see LINK{trm_del.hlp}) |
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| 99 | |
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| 100 | |
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| 101 | |
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| 102 | |
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