source: tags/arb_5.1/HELP_SOURCE/oldhelp/arb.hlp

#Please insert up references in the next lines (line starts with keyword UP)
UP      help.hlp
UP      FAQS.hlp
UP      glossary.hlp
UP      version.hlp
UP      arb_commands.hlp
UP      copyright.hlp
UP      arb.pdf
UP      changes.hlp

#Please insert subtopic references  (line starts with keyword SUB)
SUB     arb_ntree.hlp
SUB     arb_pars.hlp
SUB     e4.hlp
SUB     gde.hlp
SUB     pt_server.hlp
SUB     save.hlp
SUB     no_tree.hlp

#************* Title of helpfile !! and start of real strunk ********
TITLE           ARB: a Short Introduction

OCCURRENCE      General info

DESCRIPTION     ARB (ARBor, Latin: tree): A software environment for maintaining
                databases of molecular sequences and additional information, and
                for analyzing the sequence data, with emphasis on phylogeny
                reconstruction.

                The programs have primarily been developed for ribosomal
                ribonucleic acid (rRNA) sequences and, therefore, contain
                special tools for alignment and analysis of these structures.
                However, other molecular sequence data can also be handled.
                Protein gene sequences and predicted protein primary structures
                as well as protein secondary structures can be stored in the same
                database.

                The ARB package is designed for graphical user
                interface. Program control and data display are available in
                a hierarchical set of windows and subwindows. The majority of
                operations can be controlled using the mouse for moving the
                pointer and the left mouse button for initiating and performing
                operations

SECTION         HOW TO START

                Enter <arb> or <arb filename> to start.

SECTION         ARB MODULES

        ARB_DB

                A central database of (aligned homologous) sequences and
                additional information, taken from public databases or supplied
                by the user, is stored in a (binary or ASCII) file (*.arb).

                All ARB tools for database handling and most ARB tools
                for data analysis act directly upon the database. Any local modifications by
                individual ARB tools are immediately exported to the database
                and all other active tools.

                The database can be structured according to phylogeny or other
                user-defined criteria.

                Tools for text-oriented database searching are integrated.

        ARB_NT

                Phylogenetic trees derived from the data or imported from other
                sources are displayed within the main window. Different tree
                topologies, complete trees, and subtrees can be stored and used for
                "walking" through the database. Database entries can be
                shown with the tree on the screen or in separate windows.
                Trees can be used to define subsets of data for display
                or analysis by other ARB tools.

                Publication-ready trees can be produced by shaping the
                displayed tree topology and printing or exporting the tree to
                foreign software (TREETOOL [], XFIG []).

        ARB_EDIT

                An editor for the display of sequences and sequence-associated
                data (masks and filters, consensus sequences, higher-order structure) and
                basic editing functions is available. This tool allows manual entering of
                new sequences (with a customized keyboard, if desired); manual modification
                of alignments; search and replacement of sequence stretches; and printout of data.
                Predicted higher-order
                structure is automatically checked according to a user-provided
                mask, and may be displayed with the sequences by
                user-definable symbols.

        ARB_ALIGN

                The ARB tool for automated sequence alignment searches for the
                most similar sequences in the database and inserts the new
                sequence into an existing alignment according to primary and
                higher-order structural similarity.

        ARB_IMPORT/EXPORT

                ARB modules as well as integrated foreign software (GDE [1],
                READSEQ [2], CONVERTALIGN [3]) can be used for import and export
                of (subsets of) data in different formats, and for database
                merging.

        ARB_PROTECTION

                Up to six hierarchical protection levels can be individually
                assigned to database entries to prevent unintended modification
                or loss of data.

        ARB_NAMES

                Unique identifiers are automatically generated for the
                individual entries and stored with the database. This prevents
                multiple entries of the same data, and assignment of identical names to different data.

        ARB_PHYL

                ARB tools and integrated foreign software (PHYLIP [4], DE SOETE
                [1], fastDNAml [4]) allow calculation of similarity/distance
                matrices, conservation profiles, selection masks and phylogenetic
                tree reconstruction using different treeing approaches.

        ARB_PROBE

                Species- and group-specific probes are designed and checked by searching the complete database for unique sequence
                stretches. Potential probe or target sites are ranked by user-supplied criteria for mismatch weighing.


NOTES           Most ARB tools allow user
                input concerning database structure,
                data selection, inclusion of additional data,
                specification of analysis parameters, and design of simple
                programs for online data analysis. Default values or examples
                are included in the current release.

                Online help is available for all tools (windows).

EXAMPLES        None

WARNINGS        !!! The protection level option is only available for sequences
                in the current release !!!

                !!! The trees provided with the current release are definitely
                not optimal trees !!! However, they are useful for database walking.

BUGS            No bugs known