|
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
asigned 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 phylogentic
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.
|