| More docs on the ARB website. See also index of helppages. Last update on 22. May 2026 .

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# ARB help index List of existing helpfiles ## List of existing helpfiles
    ARB Command Interpreter (ACI)
    ARB Manuals
    ARB PARSIMONY INTRO ( Filter Weights )
    ARB Parsimony
    ARB WWW Queries
    ARB change log
    ARB environment variables
    ARB intro window (Open, merge, create ARB databases)
    ARB: Basic ARB-Shell Commands
    ARB: Database
    ARB: a Short Introduction
    ARB_EDIT4 - Sequence primary and secondary structure editor
    ARB_EDIT4 Block Operation
    ARB_EDIT4 F.A.Q.
    ARB_EDIT4 Options
    ARB_EDIT4 Replace
    ARB_EDIT4: Node Display Setup (NDS)
    ARB_GENEMAP - Gene map editor
    ARB_GENEMAP modes
    ARB_NT Main Window
    ARB_NTREE keyboard reference
    ARB_PHYLO - Create filters by base frequency
    ARB_SECEDIT - Secondary structure editor
    ARB_SECEDIT main window
    ARB_SECEDIT modes
    ARB_SECEDIT shortcut keys
    Add Marked Species
    Add Marked Species and Local Optimization
    Add Selected Species
    Add Selected Species and Local Optimization
    Add marked partial species
    Algorithm used for consensus tree
    Alignment Administration
    AxML.doc
    Bootstrap/Branchlength transfer
    Branch analysis
    CAP2
    CONCATENATION of ALIGNMENTS / SEQUENCES
    Calculate Branch Lengths
    Calculate sequence quality
    Calculate the Percentage of the Most Frequent Base
    Check and modify the consistency of two alignments
    Chimera check
    Cluster detection
    Cluster groups
    Color properties
    Colorize listed species
    Colorizing marked items / Marking colored items
    Column Statistic (Prototype)
    Column statistic
    Compare and Transfer Species Entries
    Compare tree topologies
    Configure color groups
    Consensus
    Consensus Tree
    Consensus definition
    Convert Species to SAI
    Convert fields
    Copy Species/Gene
    Copyrights
    Count Marked Species
    Count different chars/column
    Create Gene / Edit location
    Create SAI from protein secondary structure
    Create Species
    Create a Field
    Create a new input mask
    Customize Keyboard
    Customizing GDE menus
    DELETE LISTED SPECIES/GENES
    DNAml_rates
    Define Helix Symbols
    Define fields exported with gene species
    Delete Fields
    Delete Marked Species
    Delete Species/Gene
    Delete Valid Names form Database
    Design Primers
    Design Sequencing Primers
    Display options for the Residues / Bases
    Dot potentially missing bases
    E. coli Reference
    Estimate Parameters from Column Statistics
    Estimation of Bootstrap by Parsimony
    Export & import secondary structure
    Export Column statistics to GnuPlot
    Export File Formats
    Export Filter to ARB
    Export NDS List
    Export Selected Species and Sequences
    Export Tree to File
    Export to xfig
    External tools used by ARB (doc)
    Extract genes to gene-species
    FAQ: Frequently Asked Questions
    FORMAT ALIGNMENTS
    Formats
    Frame Properties
    GDE Extended Menu
    GENE INFORMATION
    GROUP MODE
    General Display Options
    General options for ARB_GENE_MAP
    Get the differences between two sequences of different databases
    Global Optimization
    Glossary
    Graph Aligner
    Group All
    Group All Except Marked
    Group all but color group
    Helix
    Help on configurations
    Hiding genes
    How is the consensus calculated?
    How to define new import formats
    How to fix an 'exec' problem ?
    How to get an initial tree
    How to save properties
    How to start ARB_EDIT4
    INFO MODE
    Import Foreign Data(bases)
    Import Valid Names from File
    Insert / Delete Column
    Insert / Delete using SAI
    Island Hopper
    Join species
    Justify branchlengths
    K.L. Optimization of the Tree
    Keep Marked
    LENGTH and MULTIFURC MODE
    LINE MODE
    LOGICAL ZOOM MODE
    Load a Tree
    Locked species information window
    MAFFT
    MARK LISTED SPECIES/GENES
    MARK MODE
    MODIFY FIELDS OF LISTED SPECIES/GENES
    MOVE MODE
    Macros
    Mapping Secondary Structural Information
    Mark by reference
    Mark color groups
    Mark duplicates in tree
    Mark genes
    Marking Gene-species
    Marking Organisms
    Marking species
    Matrices, Masks, Profiles V1.0
    Matrix settings
    Merge Similar Species
    Merge data from another ARB database
    Merge data to another ARB database
    Merge main window and workflow
    Merge two databases
    Modify SAI range
    Move node info
    MrBayes
    MrBayes (custom)
    Multifurcate tree
    Multiple ARB_NT windows
    Multiprobe Calculation
    Multiprobe parameters for calculation
    Multiproberesults
    NAME_SERVER ADMIN
    NJ bootstrap
    NOTES: dssp
    NOTES: ebi / genbank
    NOTES: fasta
    NOTES: gde_flat
    NOTES: rdp
    NOTES: universal dna
    NTREE MODES (general info)
    Nearest Neighbour Interchange
    Nearest Neighbour Interchange and K.L. Optimization
    Nearest relative search
    Nearest relatives of LISTED
    Nearest relatives of SELECTED
    Neighbour joining
    Node Display Setup (NDS)
    Old aligner from ARB_EDIT
    Optimize Database
    PT_SERVER Administration
    PT_SERVER: What Why and How
    Partial sequences
    PhyML-20130708
    Potential Probe Targets
    Predefined SRT/ACI
    Primer Design/IUPAC codes
    Primer Design/Search Parameters
    Print Ascii Files to Postscript Printer
    Print a Graphic to a Printer
    Probe Design
    Probe Match
    Probe Parameters
    Probe design (Expert)
    Probe match (Expert)
    Protection Level
    Protein Alignments
    Protein Match Settings
    Protein Viewer
    Quit
    RAxML
    ROTATE MODE
    Readme
    Readseq.help
    Realign DNA
    Regular Expressions (REG)
    Remove Marked
    Remove Zombies
    Remove/toggle bootstrap values
    Rename Species/Gene
    Reorder Fields
    Reset Logical Zoom
    Reset Physical Zoom
    Reset branchlengths
    SAI Administration
    SAI Sequence Associated Information
    SECEDIT Display settings
    SELECT A TREE
    SELECT MODE
    SET ROOT MODE
    SHOW DENDROGRAM
    SHOW IRS DENDROGRAM
    SHOW RADIAL TREE
    SPECIES INFORMATION
    SPREAD MODE
    SWAP MODE
    Save As
    Save Database
    Save matrix to file
    Save properties
    Scale branchlengths
    Scan Database for all Fields
    Search
    Search & Logical Zoom
    Search Database for Genes
    Search Database for Species
    Search List of Valid Names Manually
    Search and Replace Tool (SRT)
    Search entries existing in both databases
    Search for equal fields
    Searching
    Select Filter
    Select an Alignment
    Select species
    Select species to use for alignment adaption
    Selected Species and Cursor Position
    Selected gene
    Selections of Species (Configurations)
    Sequence color mapping
    Set Protection Level of Field of Listed Species
    Set protection level
    Show list of species
    Sort Species According Database Entries
    Sort Species According to Phylogeny
    Sort Tree Topology
    Sort tree by other tree
    Starting ARB Parsimony
    Store Tree Topologies
    Strength of base pairings
    Suggest Valid Names
    Superimposing rRNA sequence data, SAI and probes
    Synchronize species IDs
    Synchronize species IDs / ARB name server
    Synchronize species IDs before merging
    TAGS: Subfields
    TREE ADMINISTRATION
    The integrated aligners
    Toggle secondary info for SAI
    Track alignment changes
    Transfer Configurations
    Transfer SAI Entries
    Transfer Trees
    Transfer one field of selected species
    Translate DNA to Protein
    Transversion analysis
    Tree Display
    Tree Settings
    Trees
    UNMARK LISTED SPECIES/GENES
    Undo/Redo
    Ungroup All
    Unittest example helpfile
    User Defined Distance Matrix
    User mask syntax description
    User masks
    Using embedded help
    Version Info
    Visualization of Sequence Associated Information (SAI) in Primary and Secondary Editors.
    Visualization of Sequence Associated Information (SAI) of Probe Match Results.
    Visualization of Three-dimensional structure of small subunit (16S) rRNA
    WRITE TO FIELDS OF LISTED SPECIES/GENES
    WWW MODE
    What are Gene-species?
    What are Genes ?
    What are Marked Genes ?
    What are Marked Species?
    What are Organisms?
    What are Species ?
    What are color groups?
    What is an Alignment ?
    Write to File
    Write to Submission Forms
    ZOOM MODE
    clustalw [docindex]
    clustalw.doc
    clustalw_help
    dnadist.doc
    dnaml [docindex]
    dnapars
    fastDNAml.doc
    fitch.doc
    kitsch.doc
    lsadt
    neighbor.doc
    phylip
    phylip_distance [docindex]
    phyml
    proml
    protdist.doc
    protpars
    readseq [docindex]
    treepuzzle