| 1 | # main topics: |
|---|
| 2 | UP arb.hlp |
|---|
| 3 | UP arb.pdf |
|---|
| 4 | |
|---|
| 5 | # sub topics: |
|---|
| 6 | SUB trees.hlp |
|---|
| 7 | SUB helix.hlp |
|---|
| 8 | SUB props_nds.hlp |
|---|
| 9 | SUB pt_server.hlp |
|---|
| 10 | SUB extended.hlp |
|---|
| 11 | SUB species.hlp |
|---|
| 12 | SUB selected.hlp |
|---|
| 13 | |
|---|
| 14 | # format described in ../help.readme |
|---|
| 15 | |
|---|
| 16 | |
|---|
| 17 | TITLE Glossary |
|---|
| 18 | |
|---|
| 19 | SECTION What do we mean if we talk about ... |
|---|
| 20 | |
|---|
| 21 | ALIGNMENT |
|---|
| 22 | |
|---|
| 23 | Subdatabase containing homologous sequences (different |
|---|
| 24 | 'alignments' can be stored along with the species information). |
|---|
| 25 | See LINK{alignment.hlp} for more information. |
|---|
| 26 | |
|---|
| 27 | ACI |
|---|
| 28 | |
|---|
| 29 | ARB Command Interpreter. ACI is a simple programing language |
|---|
| 30 | for calculating special species information (eg. G+C Content..) |
|---|
| 31 | See LINK{aci.hlp}. |
|---|
| 32 | |
|---|
| 33 | EDGE |
|---|
| 34 | |
|---|
| 35 | Branch within a tree defined by nodes |
|---|
| 36 | |
|---|
| 37 | FIELD |
|---|
| 38 | |
|---|
| 39 | Container for 'species' associated information |
|---|
| 40 | |
|---|
| 41 | MARKED SPECIES |
|---|
| 42 | |
|---|
| 43 | Marking of 'species' defines the datasubset which is analyzed |
|---|
| 44 | by the ARB tools. |
|---|
| 45 | See LINK{mark.hlp}. |
|---|
| 46 | |
|---|
| 47 | NAMES |
|---|
| 48 | |
|---|
| 49 | There are two kinds of name fields (for species, genes, etc.). |
|---|
| 50 | |
|---|
| 51 | - name |
|---|
| 52 | |
|---|
| 53 | Identifier for 'species' entries. |
|---|
| 54 | Should be generated automatically using |
|---|
| 55 | the NAMESERVER (see LINK{sp_IDs.hlp}). |
|---|
| 56 | |
|---|
| 57 | - full_name |
|---|
| 58 | |
|---|
| 59 | User defined full name of the species,... |
|---|
| 60 | |
|---|
| 61 | NDS |
|---|
| 62 | |
|---|
| 63 | Node Display Setup: defines information which is displayed at |
|---|
| 64 | tree nodes. |
|---|
| 65 | |
|---|
| 66 | NODE |
|---|
| 67 | |
|---|
| 68 | Internal: connects branches of a tree |
|---|
| 69 | Terminal: free end of branches representing 'species' |
|---|
| 70 | |
|---|
| 71 | PT_SERVER |
|---|
| 72 | |
|---|
| 73 | Server using a special form of the ARB database for rapid |
|---|
| 74 | similarity searching (automated alignment, probe design/check) |
|---|
| 75 | |
|---|
| 76 | SAI |
|---|
| 77 | |
|---|
| 78 | Sequence Associated Information (see LINK{ad_extended.hlp}) |
|---|
| 79 | |
|---|
| 80 | SELECTED SPECIES |
|---|
| 81 | |
|---|
| 82 | See LINK{selected.hlp}. |
|---|
| 83 | |
|---|
| 84 | SPECIES |
|---|
| 85 | |
|---|
| 86 | Database entry containing a sequence and associated information. |
|---|
| 87 | Not necessarily consistent with a taxonomic species |
|---|
| 88 | |
|---|
| 89 | SRT |
|---|
| 90 | |
|---|
| 91 | Search and Replace Tool allows to search substrings in a string |
|---|
| 92 | and replace them by another substring (see LINK{srt.hlp}). |
|---|
| 93 | |
|---|
| 94 | ZOMBIES |
|---|
| 95 | |
|---|
| 96 | Zombies are references to former species in a tree, i.e. to species |
|---|
| 97 | that were in the database when the tree has been calculated, but |
|---|
| 98 | have meanwhile been deleted (see LINK{trm_del.hlp}) |
|---|
| 99 | |
|---|
| 100 | |
|---|
| 101 | |
|---|
| 102 | |
|---|
tracker (only affects html version).
