Arb help_ arb help index

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. Iphone 5 data recovery ARB_EDIT4 Options ARB_EDIT4 Replace ARB_EDIT4 mode buttons 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 partial species Add species with local optimization Add species without optimizing topology Advices Algorithm used for consensus tree Alignment Administration 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 alignments/sequences Configure color groups Consensus Consensus Tree Consensus definition Convert Species to SAI Convert fields Copy Species/Gene/Experiment Copy and Paste 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 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. Database implementation coli Reference 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 Formats Frame Properties GDE Extended Menu GROUP MODE Gene Map modes Gene information Genemap display types Genemap options Global Optimization Glossary Graph Aligner 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 Insert / Delete Column Insert / Delete using SAI Island Hopper Join species Jump to selected gene Justify branchlengths K.L. Raid 1 data recovery software optimization K.L.-mode Keep Marked Kernigham Lin (K.L.) properties LENGTH and MULTIFURC MODE LINE MODE LOGICAL ZOOM MODE Load species 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 node info MrBayes MrBayes (custom) Multifurcate tree Multiple ARB_NT windows Multiprobe Calculation Multiprobe parameters for calculation Multiprobe results NAMESERVER ADMIN 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) 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 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 Realign DNA Regular Expressions (REG) Relink tree to organisms Remove Marked Remove Zombies Remove/toggle bootstrap values Rename Species/Gene/Experiment Reorder Fields Reset Logical Zoom Reset Physical Zoom Reset branchlengths Reset optimal parsimony Reset window layout Resolve IUPAC for Probe Match SAI Administration SAI Sequence Associated Information 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 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 Searching Select Filter Select an Alignment Select display field Select or create new field Select species Select species to use for alignment adaption Selected Species and Cursor Position Selected gene 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) 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 Synchronize species IDs before merging Synchronize tree scrolling TAGS: Subfields 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 Transversion analysis Tree Settings Tree administration 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 differences to selected Visualization of Sequence Associated Information (SAI) in Primary and Secondary Editors. Seagate data recovery Visualization of Sequence Associated Information (SAI) of Probe Match Results. Database report Visualization of Three-dimensional structure of small subunit (16S) rRNA WWW MODE What are Gen
e-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