#Please insert up references in the next lines (line starts with keyword UP)
UP	arb.hlp
UP	arb.pdf

#Please insert subtopic references  (line starts with keyword SUB)
SUB	trees.hlp
SUB	helix.hlp
SUB	props_nds.hlp
SUB	pt_server.hlp
SUB	extended.hlp
SUB	species.hlp
SUB	selected.hlp

# Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain}

#************* Title of helpfile !! and start of real helpfile ********
TITLE		Glossary

SECTION         What do we mean if we talk about ...

        ALIGNMENT

                        Subdatabase containing homologous sequences (different
        		'alignments' can be stored along with the species information).
                        See LINK{alignment.hlp} for more information.

        ACI

                        ARB Command Interpreter. ACI is a simple programing language
        		for calculating special species information (eg. G+C Content..)
                        See LINK{aci.hlp}.

        EDGE

                        Branch within a tree defined by nodes

        FIELD

                        Container for 'species' associated information

        MARKED SPECIES

                        Marking of 'species' defines the datasubset which is analyzed
                        by the ARB tools.
                        See LINK{mark.hlp}.

        NAMES

                        There are two kinds of name fields (for species, genes, etc.).

                              - name

                                        Identifier for 'species' entries.
                                        Should be generated automatically using
                                        the name server.

                              - full_name

                                        User defined full name of the species,...

        NDS

                        Node Display Setup: defines information which is displayed at
        		tree nodes.

        NODE

                        Internal: connects branches of a tree
        		Terminal: free end of branches representing 'species'

        PT_SERVER

                        Server using a special form of the ARB database for rapid
        		similarity searching (automated alignment, probe design/check)

        SAI

                        Sequence Associated Information

        SELECTED SPECIES

                        The 'selected species' is that ONE species which has been selected
                        by using any of the following actions

                                - ARB_NTREE/Search + click onto one search result
                                - ARB_MERGE/Transfer species + click onto one search result
                                  (here there is one selected species in each of the two involved DBs)
                                - clicking on the species name in the tree display in ARB_NT
                                - placing the cursor into the sequence of a species in ARB_EDIT4

                        The currently selected species will be displayed in the 'Species info window'

        SPECIES

                        Database entry containing a sequence and associated information.
        		Not necessarily consistent with a taxonomic species

        SRT

                        Search and Replace Tool allows to search substrings in a string
        		and replace them by another substring (see LINK{srt.hlp}).

        ZOMBIES

                        Zombies are references to former species in a tree, i.e. to species
                        that were in the database when the tree has been calculated, but
                        have meanwhile been deleted (see LINK{trm_del.hlp})