| More docs on the ARB website. See also index of helppages. Last update on 14. Feb 2019 .

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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