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