ARB Command Interpreter (ACI)
ARB Manuals
ARB NAMESERVER / Synchronize IDs
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 mode buttons
ARB_EDIT4: Node Display Setup (NDS)
ARB_GENEMAP - Gene map editor
ARB_GENEMAP modes
ARB_NT Main Window
ARB_PHYLO - Create filters by base frequency
ARB_SECEDIT - Secondary structure editor
ARB_SECEDIT main window
ARB_SECEDIT modes
ARB_SECEDIT shortcut keys
Accessibility SAIs
Add marked partial species
Add species with local optimization
Add species without optimizing topology
Advices
Algorithm used for consensus tree
Alignment Administration
Auto-adjust roots of trees
AxML.doc
Bootstrap display settings
Bootstrap/Branchlength transfer
Branch analysis
Calculate Branch Lengths
Calculate sequence quality
Calculate the Percentage of the Most Frequent Base
Change molecule
Check and modify the consistency of two alignments
Chimera check
Cluster detection
Cluster groups
Collapse/expand tree
Color properties
Colorize listed items
Colorizing marked items / Marking colored items
Column Statistic (Prototype)
Column statistic
Compare and Transfer Species Entries
Compare taxonomy
Compare tree topologies
Concatenation of sequences
Configure color groups
Consensus
Consensus Tree
Consensus definition
Convert Species to SAI
Convert fields
Copy Species/Gene/Experiment
Copy and Paste
Copyrights and licenses
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
Create groups using field content
Customize Keyboard
Customizing GDE menus
DNAml_rates
Database field shader
Define Helix Symbols
Define fields exported with gene species
Delete Fields
Delete Listed
Delete Marked Species
Delete Species/Gene/Experiment
Delete Valid Names form Database
Design Primers
Design Sequencing Primers
Determine sequence changes between different databases
Display options for the Residues / Bases
Dot potentially missing bases
E. coli Reference
Edit bootstraps
Edit color ranges
Edit config entries
Editor configurations
Estimate Parameters from Column Statistics
Estimation of Bootstrap by Parsimony
Experiment information
Expert tree settings
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 to xfig
Export tree to file
External tools used by ARB (doc)
Extract genes to gene-species
FAQ: Frequently Asked Questions
FORMAT ALIGNMENTS
Fasttree
Field transfer sets
Formats
Frame Properties
GDE Extended Menu
GROUP MODE
Gene Map modes
Gene information
Genemap display types
Genemap options
Global Optimization
Glossary
Graph Aligner (SINA)
Helix
Hiding genes
Highlight configurations in tree
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
Import from calc-sheets
Import/export format management
Insert / Delete Column
Insert / Delete using SAI
Island Hopper
Join species
Jump to selected gene
Justify branchlengths
K.L. optimization
K.L.-mode
Keeled groups
Keep Marked
Kernigham Lin (K.L.) properties
LENGTH and MULTIFURC MODE
LINE MODE
LOGICAL ZOOM MODE
Load species/SAI into running editor
Load tree from file
Load/save item colorsets
Local optimization
Locked species information window
MAFFT
MARK MODE
MOVE MODE
Macros
Mapping Secondary Structural Information
Mark Listed Unmark Rest
Mark by reference
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 tagged fields
Merge two databases
Modify SAI range
Modify fields of listed
Move groups
Move node info
MrBayes
MrBayes (custom)
Multifurcate tree
Multiple ARB_NT windows
Multiprobe Calculation
Multiprobe parameters for calculation
Multiprobe results
Muscle
NJ bootstrap
NNI (Nearest Neighbour Interchange)
NNI+KL-mode
NNI-mode
NOTES: dssp
NOTES: ebi / genbank
NOTES: fasta
NOTES: gde_flat
NOTES: rdp
NOTES: universal dna
NTREE MODES (general info)
Nameserver admin
Nearest relative search
Nearest relatives of LISTED
Nearest relatives of SELECTED
Neighbour joining
New genemap view
Node Display Setup (NDS)
Old aligner from ARB_EDIT
Optimize database compression
PT_SERVER Administration
PT_SERVER: What Why and How
Parsimony value
Partial sequences
PhyML-20130708
Potential Probe Targets
Predefined SRT/ACI
Primer Design RESULT
Primer Design/IUPAC codes
Primer Design/Search Parameters
Print Ascii Files to Postscript Printer
Print a Graphic to a Printer
ProbCons
Probe Collection Matching
Probe Design
Probe Design parameters
Probe Match
Probe design (Expert)
Probe match (Expert)
Property/settings configurations
Protection Level
Protein Alignments
Protein Match Settings
Protein Viewer
Questions
Quit
RAxML
RAxML 8 (DNA)
RNA3D Display Options
ROTATE MODE
Randomize topology
Re-repair database
Readme
Readseq.help
Realign DNA
Recommended way to maintain amino acid alignments
Regular Expressions (REG)
Relink tree to organisms
Remove Marked
Remove Zombies
Remove bootstrap values
Rename Species/Gene/Experiment
Rename taxonomic groups
Reorder Fields
Reset Logical Zoom
Reset Physical Zoom
Reset branchlengths
Reset optimal parsimony
Reset window layout
Resolve IUPAC for Probe Match
SAI (Sequence associated information)
SAI Administration
SAI calculator
SECEDIT bond definitions
SECEDIT display options
SELECT A TREE
SELECT MODE
SET ROOT MODE
SHOW DENDROGRAM
SHOW IRS DENDROGRAM
SHOW RADIAL TREE
SPECIES INFORMATION
SPREAD MODE
SWAP MODE
Save / load secondary structure
Save Database
Save matrix to file
Save properties
Save properties of ARB_EDIT4
Scale branchlengths
Scan Database for all Fields
Search & Logical Zoom
Search & Replace in block
Search Database for Experiments
Search Database for Genes
Search Database for Species
Search List of Valid Names Manually
Search and Replace Tool (SRT)
Search and highlight sequence patterns
Search entries existing in both databases
Search for equal fields
Search taxonomic groups
Searching
Select Filter
Select an Alignment
Select display field
Select or create new field
Select species
Select species to use for alignment adaption
Select trees to search
Selected gene
Selected species
Sequence background color priority
Sequence color mapping
Set Protection Level of Field of Listed Species
Set protection level
Show list of species
Show only differences to selected
Sort Species According Database Entries
Sort Species According to Phylogeny
Sort Tree Topology
Sort tree by other tree
Species flags
Species selections (=editor configurations)
Split sequences
Start a console
Starting ARB Parsimony
Store Tree Topologies
Strength of base pairings
Suggest Valid Names
Superimposing rRNA sequence data, SAI and probes
Sync ARB_SECEDIT colors with ARB_EDIT4
Synchronize species IDs
Synchronize species IDs before merging
Synchronize tree scrolling
TAGS: Subfields
Test export filter
Test import filter
The integrated aligners
Toggle secondary info for SAI
Topology shader
Track alignment changes
Transfer Configurations
Transfer SAI Entries
Transfer Trees
Transfer one field of listed species
Transfer one field of the selected species
Translate DNA to Protein
Translation tables
Transversion analysis
Tree Settings
Tree administration
Tree display keyboard reference
Tree marker display setup
Tree optimization
Tree shading
Trees
Undo/Redo
Unittest example helpfile
Unmark Listed Mark Rest
User Defined Distance Matrix
User mask syntax description
User masks
Using embedded help
Validate taxonomy (SATIVA)
Version Info
View ARB logs
View differences to selected
Visualization of Three-dimensional structure of small subunit (16S) rRNA
Visualize SAIs at probe match targets.
Visualize SAIs in editors.
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
Write to fields of Listed
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