Last updated on 06.Apr 2017

The ARB structure editor

  1. How to start the editor
  2. How to name and store a "selection"
  3. How to move in the "editor" window (ARB_EDIT4)
  4. How to position the "editor"s cursor
  5. How to manually modify the relative "species" or character positioning (alignment)
    1. Two procedures are available to move valid characters:
  6. How to change valid characters (modify the sequences)
    1. The keyboard can be customized for editing sequences:
    2. Multiple editing operations
  7. How to define and visualize search strings
    1. The settings for search string visualization can be defined in the "search string" area in the upper part of the "editor" window (ARB_EDIT4).
  8. How to handle "consensus" sequences
  9. How to create new species and groups
  10. How to merge individually stored sequence parts
  11. How to import or remove sequences from the editor
  12. How to perform the "block" operations
    1. The "block" block operations provide access to (parts of) sequences of "selected species" independently of their "marked" status.
  13. How to use the "fast aligner"
    1. Selection of "species"/sequences to align
    2. Selection of "species"/sequences as templates
    3. Definition of sequence region to align
  14. How to virtually hide gaps or characters
  15. How to undo/redo operations

  1. How to start the editor

    The editor is started from the main window (ARB_NT)
    First a valid alignment (RNA, DNA, protein) has to be selected (left mouse button) from the list popping up after pressing (left mouse button) on the "alignment" button (third from left in the firstline of buttons in the upper section of the main window)
    To start press (left mouse button) on the "editor" button (fifth from left in the second line of buttons in the upper section of main window) in the main window (ARB_NT).
    The editor will be started visualizing the sequences of the "marked" "species" stored in the specified alignment. The order (top to buttom) corresponds to that of the corresponding organisms in the tree currently visualized in the main window.
    Alternatively select one of three starting modes from the pop up menu activated by clicking (left mouse button) on ´Sequence´ (third from left in the menu line of the main window) or using the short cut ´Alt s´ ´Edit Marked Sequences Using Selected Species and Tree´: same function as pressing the ´aligner´ button as described above. ´Edit Marked Sequences (plus sequences aside)´: the "marked" and the specified number (type to the editing area in the ´Enter number of extra species´ pop up window) of "unmarked" next neighboring sequences are visulalised in the order of the respective "species" in the tree currently visualized in the main window. ´Edit Sequences Using Earlier Selection´: sequences are selected and ordered as specified in a previously defined, named and stored "selection" which has to be selected (left mouse button) from the ´SELECT A CONFIGURATION´ pop up window.

  2. How to name and store a "selection"

    Select (left mouse button) ´Save Configuration as´ from the pop up menu activated by pressing (left mouse button) on ´File´ in the menu line of the "editor" window (ARB_EDIT4), alternatively use short cut (Alt f). Type a name for the "selection" to the editing area ("Save Editor Configuration as") of the "SAVE A CONFIGURATION" pop up window. Subsequently press (left mouse button) the ´Start´ button.
    Note: any changes made in the editor are not permanent until the underlying ARB database is stored independently of saving a selection.

  3. How to move in the "editor" window (ARB_EDIT4)

    Move the visualization area one character or line left/right or up/down by pressing the corresponding arrow heads in the scroll bar areas. Move the visualization area (halve window length/height) left/right or up/down by clicking (left mouse button) left/right or above/below the corresponding scroll bar, respectively. Place the mouse cursor in the "sequence" area, press the right mouse button and drag the desired direction to move the visualization area.

  4. How to position the "editor"s cursor

    Place the mouse cursor somewhere in the "sequence" (not in the "name") area and position the "editor" cursor by presing the left mouse button.
    Note: the cursor is positioned between the sequence characters and numbering concerns the character next right to the cursor.
    The cursor symbol can be changed by activating the pop up menu by clicking (left mouse button) on ´Properties´ in the menu line of the "editor" window (ARB_EDIT4) or using the short cut ´Alt p´ and subsequently selecting ´Change Cursor´ from the pop up menu or using short cut ´Alt c´ while this menu is open.
    The "editor" cursor can be moved to the next valid (i.e. not a "gap" symbol" as defined character right/left or up/down by pressing ´Ctrl´ and the respective ´arrow´ key.
    Note: the current cursor position is monitored in the respective sub windows ´Position´ (absolute alignment position: Characters and gap symbols), ´E.coli´ (equivalent position in the E. coli reference sequence), ´Base´ (position in the respective sequence; only characters, no gaps), ´IUPAC´: character at the respective position (ambiguity symbols are resolved), ´Helix #´ helix number for base paired positions (indicated by "helix" symbols below the respective cursor.
    If the the "editor"s cursor is positioned somewhere in the "sequence" area the position can be changed by moving the mouse cursor in one of the monitoring subwindows, typing a position (helix) number, and moving the mouse cursor back to the "sequence" area.
    Note: using ´Helix #´ monitoring subwindow is active only if the position next right to the "editor"s cursor is base paired (helix symbol below the respective character).

  5. How to manually modify the relative "species" or character positioning (alignment)

    To move "species"/sequences activate the ´MOVE´ mode by left mouse button click on the ´MOVE´ button in the left vertical panel of the "editor" window(ARB_EDIT4) and move by left mouse button click on an entry in the ´name´ area and dragging to the desired position.
    Note: any rearrangements will be lost unless the editor configuration is saved (see above)
    Ensure that the "Align/Edit" button is set to ´Align´, press (left mouse button) it to change if necessary.
    Note: Changes of character positioning are only allowed if the "rights" set for the editor (press - left mouse button - the ´Protect´ selection box and select a level) equals or is higher than the "protection level" of the individual sequences.
    The latter can be changed by positioning the cursor within the respective sequence, activate a pop up menu by clicking (left mouse button) on ´Edit´ in the menu line of the "editor" window (ARB_EDIT4) or by using the short cut ´Alt e´, activate the protection pop up menu by clicking on ´Set protection of current´ or using short cut ´Alt p´ and select the desired protection level from the nest pop up menu.
    Note: the application of different protection levels for e.g. perfect and preliminary aligned sequences helps to prevent unwanted changes of the latter resulting from misplaced "editor" cursor!
    The "Align" mode allows to insert or remove gap symbols (defined in the "property settings") as well as to move, however, not to change, insert delete characters.
    Insert gap symbols by typing the respective symbol after placing the "editor"s cursor.
    Note: Typing a gap symbol (defined in the "property settings") within a stretch of alternative gap symbols will change the whole stretch (between the next neighboring valid characters) to the typed symbol.
    Typing the same symbol again will insert a new gap.
    Remove gap symbols left or right to the positioned cursor by pressing the backspace or delete key respectively.
    Two procedures are available to move valid characters:
    Position the "editor"s cursor. If there are gap symbols neighboring the cursor pressing ´Alt left/right arrow key´ fetches the next valid character left right to the cursor position, respectively. If there are valid characters neighboring the cursor pressing ´Alt left/right arrow key´ moves the respective neighboring character to the next right/left (!) valid character, respectively.
    Note: the latter procedure only works if there are gap symbols in between the respective valid characters.
    Contiguous stretches of valid characters can be moved by placing the "editor"s cursor next left/right to it and pressing ´Shift and right/left arrow keys´.
    Note: this procedure only works if there are gap symbols neighboring the stretch towards the desired direction of movement.
    Blocks of stretches of valid characters can be moved left/right after selecting by positioning the mouse cursor to a corner of the desired block, pressing the right mouse button and defining a rectangle by dragging the cursor to the desired position and releasing the right mouse button. The defined block can be moved right/left by clicking (left mouse button) on ´Block´ in the menu line of the "editor" window (ARB_EDIT4) or using short cut ´Alt b´ and selecting (left mouse button) ´Shift right/left´ from the pop up menu.
    Note: this procedure only works if there are gap symbols neighboring the block towards the desired direction of movement. These gap symbols have to be included in the rectangle described above.

  6. How to change valid characters (modify the sequences)

    Ensure that the "Align/Edit" button is set to ´Edit´, press (left mouse button) it to change if necessary. The "Insert" or "Replace" mode can be selected by pressing (left mouse button) the ´Edit/Replace´ button. The active mode is indicated on that button.
    Note: Changes of character positioning are only allowed if the "rights" set for the editor (press - left mouse button - the ´Protect´ selection box and select a level) equals or is higher than the "protection level" of the individual sequences.
    The "rights" can be set independently for the "edit" and "align" modes.
    The "protection level" of the sequences can be changed by positioning the cursor within the respective sequence, activate a pop up menu by clicking (left mouse button) on ´Edit´ in the menu line of the "editor" window (ARB_EDIT4) or by using the short cut ´Alt e´, activate the protection pop up menu by clicking on ´Set protection of current´ or using short cut ´Alt p´ and select the desired protection level from the nest pop up menu.
    For changing valid characters position the "editor"s cursor.
    Pressing (left mouse button) the ´back space´ or ´delete´ key removes the character next left or right to the cursor, respectively.
    Note: the rest of the sequence right to the deleted character is moved to the left (!) the alignment might get disturbed.
    Valid characters can be changed ("edit" mode) or inserted ("insert" mode) by typing any character. The operation concerns the position next right to the cursor.
    Note: to be able to type numbers the multiple operation facility (see below) has to be switched off (otherwise the next operation would be performed several times according to the number typed).
    Click (left mouse button) on the ´Properties´ in the menu line of the "editor" window (ARB_EDIT4) or use short cut ´Alt p´ to pop up the ´EDIT4 Options´ window and uncheck the ´Use digits to repeat edit commands?´ checkbox.
    Alternatively, visualize the "search string" area in the upper part of the "editor" window (ARB_EDIT4) by pressing the button labelled with a black triangel and switch off the "repeat" mode by pressing (left mouse button) the ´REPEAT´ button.
    The inactive status is indicated by "striked" text on the button.
    The typing orientation (left to right/right to left) is indicated by the arrow on the 5´...3´ button in the upper panel of the "editor" window (ARB_EDIIT4) and can be changed by pressing (left mouse button).
    Note: the positions of targeted characters are changed consequently with respect to that of the "editor"s cursor.
    The keyboard can be customized for editing sequences:
    Click (left mouse button) on ´Properties´ in the menu panel of the "editor" window (ARB_EDIT4) or use short cut ´Alt p´ and select ´Key Mappings ...´ from the pop up menu or use short cut ´Alt k´
    Move the mouse cursor to the respective editing subwindow in the ´KEY MAPPINGS´ pop up window and type the key and its meaning to the horizontally neighbored ´keyboard´ and ´ASCII´ editing subwindows, respectively. Case sensitive (!)
    The keymapping is enabled or disabled by checking or unchecking the ´Enable Mapping´ check box of the ´KEY MAPPINGS´ pop up window.
    Alternatively, visualize the "search string" area in the upper part of the "editor" window (ARB_EDIT4) by pressing the button labelled with a black triangel and set the "key mapping" mode by pressing (left mouse button) the ´KEYMAP´ button.
    The inactive status is indicated by "striked" text on the button.
    Multiple editing operations
    Any described editing such as inserting, deleting, changing, and moving characters can be performed as multiple operations by typing a number before executing the respective procedure.
    Note: the multiple operation mode has to be in activated status.
    To activate, click (left mouse button) on the ´Properties´ in the menu panel of the "editor" window (ARB_EDIT4) or use short cut ´Alt p´ to pop up the ´EDIT4 Options´ window and check the ´Use digits to repeat edit commands?´ checkbox.
    Alternatively, visualize the "search string" area in the upper part of the "editor" window (ARB_EDIT4) by pressing the button labelled with a black triangel and switch on the "repeat" mode by pressing (left mouse button) the ´REPEAT´ button.
    The inactive status is indicated by "striked" text on the button.

  7. How to define and visualize search strings

    The settings for search string visualization can be defined in the "search string" area in the upper part of the "editor" window (ARB_EDIT4).
    Visualize the "search string" area in the upper part of the "editor" window (ARB_EDIT4) by pressing (left mouse button) the button labelled with a black triangel.
    Search strings can be typed to the tree editing subwindows ´User1´ ´User2´ and ´Probe´ in the "search string" area in the upper part of the "editor" window (ARB_EDIT4).
    Move the mouse cursor to the respective editing subwindow and type a search string
    Note: the ´Probe´ subwindow is automatically used by the ´Probe_Match´ tool. It is recommended not to use this subwindow while performing probe design or evaluation.
    For visualization of the search string check the check box assigned to the respective subwindow (right in the same panel)
    Any occurrence of the string will be highlighted in the "sequence" area of the of the "editor" window (ARB_EDIT4) by a corresponding background color.
    To move to the next or previous occurrence press (left mouse button) the ´NEXT´ or ´LAST´ button assigned to the respective subwindow (right in the same panel)
    Note: the "editor"s cursor has to be placed somewhere in the "sequence" area of the of the "editor" window (ARB_EDIT4).
    To customize the search and visualization settings and/or establish permanent lists of search strings press (left mouse button) the "setting" button assigned to the respective subwindow (right in the same panel, between ´NEXT´ and the "visualization´ checkbox) to pop up the ´...Search´ customization window.
    Lists of search strings can be typed to the ´Search Patterns´ editing subwindow after moving the mouse cursor to it.
    Note: "?" can be used as a single letter wild card.
    Different search strings have to be separated by "," or by typing carriage return.
    Comments to the individual strings can be typed to the same line separated from the corresponding string by "#".
    The list can be stored and reloaded as an ASCII file independently from the respective ARB database by pressing (left mouse button) the ´SAVE´ and ´LOAD´ button, respectively. File name and path have to be defined in the ´Load ... Search Parameters´ and ´Save ... Search Parameters´ window, respectively.
    The search and visualization parameters can be customized by checking/unchecking an appropriate selection of checkboxes in the right half of the ´...Search´ customization window.
    The meaning of checked the boxes:
    ´Show?´: visualization of the string by background color in the in the "sequence" area of the of the "editor" window (ARB_EDIT4).
    ´Auto jump?´: when checking the ´Show?´ box the "sequence" area of the of the "editor" window (ARB_EDIT4) will be centered on the first occurrence of the search string.
    ´Open folded´: if the search string occurs in sequences which are hided by group compression the respective group will be "unfolded"
    ´Ignore gaps in sequence?´: gap symbols in the target sequence will not be taken into consideration for sequence comparison.
    ´Ignore gaps in pattern?´ gap symbols in a search string will not be taken into consideration for sequence comparison.
    ´Treat T as U´: T/t and U/u will be regarded as identical
    ´Ignore case?´: search will be performed case insensitive
    ´Search for complement?´: target strings (directly) complementary to the search string will be highlighted in addition.
    ´Search for reverse?´: tartget strings representing the (5´-3´ reverted search string will be highlighted in addition.(
    Note: checking both the "Search for complement?" and the "Search for reverse?" boxes results in highlighting reverse complementary targets in addition.(ARB_EDIT4).
    ´Exact?´ only reverse complementary targets will be highlighted, however not targets identical to the search string.
    Pressing (left mouse button) the respective toggles assigned to ´Minimum´ and ´Maximum´ results in exclusive highlighting of imperfect targets containing the defined minimum number of "mismatches" or the additional highlighting of imperfect targets containing the defined maximum number of "mismatches"
    Note: The "mismatched" positions can be highlighted by different background color..
    Pressing (left mouse button) the ´LAST´/´NEXT´ button will center the "sequence" area of the of the "editor" window (ARB_EDIT4) on the previous or next target in relation to the position of the "editor"s cursor, respectively.
    Independent lists of search strings can be established and permanently stored activating the respective ´...Search´ customization window of ´Primer (local)´, ´Primer (region)´, ´Primer (global)´, ´Signature (local)´, ´Signature (region)´, ´Signature (global)´´.

  8. How to handle "consensus" sequences

    If the "editor" is started with the option ´Edit Sequences Using Selected Species and Tree´ (see above) the (phylogenetic) groups (if) defined in the currently visualized tree of the "main window" (ARB_NT) are indicated by brackets combining the names of the group members in the "names" area of the "editor" window (ARB_EDIT4).
    The respective "group name" along with a consensus sequence is shown on the top of the ingroup "names" and sequences in the "name" and "sequence" area respectively.
    These groups can be shown in "compressed" mode - the whole group is represented by the group name and the corresponding consensus sequence only - or "unfolded" mode - all names and sequences as well as the group name and consensus sequence shown - by clicking (left mouse button) on the black triangle located at the upper edge of the individual group brackets.
    To set the parameters for consensus calculation and visualization display the ´Properties´ menu by clicking on ´Properties´ in the menu panel of the "editor" window (ARB_EDIT4) or use the short cut ´Alt p´ and select ´Consensus ...´ to display the ´EDIT4_Consensus_Definition´ pop up window.
    A threshold value for visualizing gap symbol consensus by a dash in the consensus sequence can be defined by moving the mouse cursor to the ´threshold for gaps´ editing subwindow and typing a value (% of sequences in the group).
    This function is switched on or off by pressing (left mouse button) one of the respective toggles in the ´What to Do with Gaps?´ subwindow.
    Pressing (left mouse button) one of the ´on´ ´off´ toggles in the ´Simplify Using IUPAC´ subwindow allows to switch between base/ambiguity or amino acid/biochemical class symbol visualization modes.
    Note: Pressing (left mouse button) the ´show IUPAC...´ button displays the ambiguity codes in the ´Show_IUPAC´ pop up window.
    A Threshold for contributing of sequence characters for IUPAC visualization can be defined by moving the mouse cursor to the ´threshold for character´ editing subwindow and typing a value (% of sequences in the group).
    Threshold values for visualization of the consensus sequence characters and symbols can be defined by moving the mouse cursor to the ´upper´ and ´lower´ editing subwindows of the ´Show as UPPER or lower Case?´ area and typing a value (% of sequences in the group)
    Note: Positions at which none of the two threshold values is verified are represented by dots in the consensus sequence.
    Checking or unchecking (left mouse button) of the ´Display consensus?´ box at the bottom of the ´EDIT4_Consensus_Definition´ window allows to visualize or hide the consensus sequence in the "editor" (ARB_EDIT4) window.
    Alternatively, the visualization of concensus sequences in the "editor" (ARB_EDIT4) window can be enabled or disabled in the "search string" area in the upper part of the "editor" window (ARB_EDIT4).
    Visualize the "search string" area in the upper part of the "editor" window (ARB_EDIT4) by pressing (left mouse button) the button labelled with a black triangel.
    Press (left mouse button) the ´CONS´ button in the "search string" area in the upper part of the "editor" window (ARB_EDIT4).
    Note: The disabled status of consensus visualization id indicated by striked text on the ´CONS´ button.

  9. How to create new species and groups

    New species (empty line in the "sequence" area of the "editor" (ARB_EDIT4) assigned to a new name in the "name" area can be generated by clicking on ´Create´ in the menu panel or using short cut ´Alt c´, subsequently selecting ´Create New Species´ from the pop up menu, and finally typing a name to the ´Please enter the FULL_NAME of the new species´ editing subwindow in the ´Create_species´ pop up window.
    Note: typing of a "full_name" i.e. genus and species (non-taxonomic names such as "bacterial species" or "environmental clone" are also accepted) is necessary to allow the "ARB_NAME_SERVER" to keep ARB database internal ID´s (´names´) unique and consistent.
    Before creating a new group the respective group members have to be selected by clicking (right mouse button !) on the names in the "name" area of the "editor" window (ARB_EDIT4).
    Note: the background color for highlighting selected Species or sequences can be defined in the ´Properties´ (see below).
    New groups (including group brackets and consensus) comprising selected "species" can be created by clicking on ´Create´ in the menu panel or using short cut ´Alt c´, subsequently selecting ´Create new group´ from the pop up menu, and finally typing a name to the ´Enter name for the new group´ editing subwindow in the ´ENTER_A_STRING´ pop up window.
    Note: the new group is automatically moved to the upper editing area of the "editor" (ARB_EDIT4) window in compressed mode

  10. How to merge individually stored sequence parts

    Create a new group (see above) comprising all partial sequences
    If necessary, correct primary structures and alignment of the partial sequence data (see above).
    Note: visualization of the consensus in IUPAC mode helps to localite inconsistencies of the partial sequences.
    Create a new "species" based upon the consensus sequence by clicking on ´Create´ in the menu panel or using short cut ´Alt c´, subsequently selecting ´Create new species from consensus´ from the pop up menu, and finally typing a name to the ´Please enter the FULL_NAME for the new species´ editing subwindow in the ´Create new species from consensus´ pop up window.
    Note: typing of a "full_name" i.e. genus and species (non-taxonomic names such as "bacterial species" or "environmental clone" are also accepted) is necessary to allow the "ARB_NAME_SERVER" to keep ARB database internal ID's (´names´) unique and consistent.
    Typing to the ´ Replace ...´ subwindows of the ´Create new species from consensus´ window defines how gap symbols of the consensus sequence should be represented in the sequence of the new species.
    Note: ARB internal standard (not mandatory) is to indicate (real) a alignment gaps by a hyphen while missing sequence information is indicated by dots.
    Check the corresponding checkboxes in the ´Create new species from consensus´ window to convert lower case characters to upper case and to define "leader" and "trailer" symbols if desired.
    Presing the ´Merge from all in group´ button n the ´Create new species from consensus´ window allows to handle the transfer of the descriptive information stored in the respective ARB data base fields to the new species.
    Select from the pop up menu whether the information of all "species" representing the partial sequences should be merged in the data base fields of the new species (´Merge from all in group´ or the information of only one selected species should be transferred (´Copy from current species´).
    Note: the positioning of the "editor"s cursor defines the "current species" and consequently has to be placed properly.

  11. How to import or remove sequences from the editor

    Marked species and the associated sequences not present in the current editor window can be imported by clicking (left mouse button) on ´Edit´ in the menu panel of the "editor" (ARB_EDIT4) window or using short cut ´Alt e´ and selecting ´Load marked species´ from the pop up menu or using short cut ´Alt m´.
    The "current species" will be imported by clicking (left mouse button) on ´Edit´ in the menu panel of the "editor" (ARB_EDIT4) window or using short cut ´Alt e´ and selecting ´Load current species´ from the pop up menu or using short cut ´Alt g´.
    Note: the "current species" is that which is selected by the "info" tools of the main window (ARB_NT) (see elsewhere).
    To remove a species and its sequence from the "editor" window (ARB_EDIT4) activate the ´KILL´ button in the left vertical panel by presing (left mouse button) and click (left mouse button) on the respective entry in the "name" area.
    Note: the species/sequence is removed from the current editor, however, not from the underlying ARB data base.

  12. How to perform the "block" operations

    The "block" block operations provide access to (parts of) sequences of "selected species" independently of their "marked" status.
    Note: here, selecting of full or parts of sequences is done by click (right mouse button !) on the respective entries in the "name" area of the "editor" window (ARB_EDIT4) or clicking (right mouse button !) and dragging in one or more contiguous sequences, respectively.
    Note: the background color for highlighting selected Species or sequences can be defined in the ´Properties´ (see below).
    The selected (parts) of sequences can be reverted and/or complemented, changed with respect to case or character state by click (left mouse button) on ´Block´ in the menu panel of the "editor" window (ARB_EDIT4) or using short cut ´Alt b´ and selecting the respective operation (´Lower case´, ´, Upper case´, ´Reverse Complement´, ´Complement´, ´Unalign´, ´Replace´ from the pop up menu or using short cuts ´Alt l´, .´Alt u´, ´Alt a´, ´Alt r.´.

  13. How to use the "fast aligner"

    To adjust the parameters for automated sequence alignment click (left mouse button) on ´Edit´ in the menu panel of the "editor" window (ARB_EDIT4) or use short cut ´Alt e´ and select (left mouse button) ´Fast Aligner´ from the pop up menu or use short cut ´Ctrl a´.
    Define the selection of "species"/sequences to align, reference "species"/sequences as templates, and the primary structure regions to align by presing one of three respective toggles in each of the ´Align´, ´Reference´, and ´Range´ areas of the ´Fast_Aligner´ window.
    Selection of "species"/sequences to align
    The current species is defined by positioning the "editor"s cursor in the "sequence" area of the "editor" window (ARB_EDIT4) or typing the respective ARB ID (´name´) in the ´Current Species´ editing subwindow.
    Marking of species can be performed with the respective tools of the main window (ARB_NT) (see elswhere) or by activating (left mouse button click) the ´MARK´ button in the left vertical panel of the "editor" window (ARB_EDIT4) and clicking (left mouse button) on the small rectangles left to the entries in the "name" area (marked status is indicated by filled rectangles.
    Selecting of species is achieved by right mouse button click on entries in the "name" area of the "editor" window (ARB_EDIT4)
    Selection of "species"/sequences as templates
    Define a single "species"/sequences as template by typing an ARB ID (´name´ to the ´Species by name´ editing subwindow of the ´Fast_Aligner´ window.
    Alternatively, place the "editor%gf;s cursor to the reference sequence in the "sequence area" of the %gf;editor" window (ARB_EDIT4) and press (left mouse button) the ´Copy´ button in the ´Fast_Aligner´ window.
    For automated search for the most similar template sequences using the ´PT_SERVER´ an appropriate server (see elsewhere) has to be chosen from the list popping up after pressing (left mouse button) the ´localhost: ...´ button.
    Note: using a higher ´Number of relatives to use´ is recommended if the PT_SERVER contains also incomplete sequences.
    Definition of sequence region to align
    ´Positions around cursor´ defines the sequence region which can be touched by the aligner
    Note: the "editor%gf;s cursor has to be properly placed in the sequence to align and the region defined in such a way that there is sufficient space for the aligner to move characters (no character is allowed to be moved outside the defined region !)
    The ´selected´ range is defined by the rectangle generated by right mouse button click and dragging in the "sequence" area of the "editor" window (ARB_EDIT4)
    Note: the region has to be defined in such a way that there is sufficient space for the aligner to move characters (no character is allowed to be moved outside the defined region !)
    Note: The %gf;rights" of the aligner have to be equal or higher than the "protection level" of the sequences to align.
    Click (left mouse button) on the ´Protection´ button and select an appropriate level from the list popping up.
    Choose one of three offered modes to handle the problem of reverse complemented sequence data by clicking (left mouse button) on the ´Turn check´ button of the ´Fast_Aligner´ window and selecting from the list popping up.
    Note: it is recommended to choose ´No report´ from the list "under" the ´Report´ button and uncheck the ´Show messages ..´ box.

  14. How to virtually hide gaps or characters

    Click (left mouse button) on ´Properties´ in the menu panel of the "editor" window (ARB_EDIT4) or use short cut ´Alt p´ and select ´Options´ fromthe displayed menu.
    Press (left mouse button) one of the left three toggles in the ´Online Sequence Compression´ area of the ´EDIT4_Options´ window to visualize uncompressed sequences (´Show all gaps´), virtually reduce the "length" of gaped regions (´Show some gaps´), or virtually hide all gaps which are common to the selection of sequences in the current editor (´hide all gaps´)
    In the ´Hide all gaps´ mode one of the two toggles inthe right of ´Online Sequence Compression´ area of the ´EDIT4_Options´ window has to be pressed (left mouse button) to either ´Hide no nucleotides´ or virtually remove even columns at which a fraction of the sequences in the current editor carry valid characters.
    Threshold value (% of all sequences in the current editor) has to be defined by typing it to the ´% Nucleotides´ edition subwindow of the ´EDIT4_Options´ window.
    Note: compresion mode should not be activated when performing major rearrangements of the alignment.
    Identical characters in a given reference sequence (place the "editor"s cursor in the "sequence" area) can be hided in all others by left mouse button click on ´Edit´ in the menu panel of the "editor" window (ARB_EDIT4) or using short cut ´Alt e´ and select ´Show only Differences to Selected´ or using short cut ´Alt d´.
    Note: this mode can be switched off by by left mouse button click o n ´Edit´ in the menu panel of the "editor" window (ARB_EDIT4) or using short cut ´Alt e´ and select ´Show all Bases´ or using short cut ´Alt a´.

  15. How to undo/redo operations

    Press the ´Undo´ or ´Redo´ buttons
    Note: press the respective button several times if you don't see the desired effect.


If you did not find a solution here please refer to the various manuals regarding ARB installation and usage. If that did not help please feel free to