Alignment Editor Program Ver.1.50

	<User's Manual of Alignment Editor Program>

1.  Environment

  This program works on X-window x11r3 or a newer version.
  X-server should be prepared before running this program.
  Color display with more than eight color planes (256 colors) is required.
  Users have to set the environment variable as follows:
          setenv XENVIRONMENT aedit.res

  These files are available in the directory where 'aedit' is executed:
	  aedit.res: for arrangement of window resource
	  prosite.dat: protein motif database
	  user.dat: user defined motif database

2.  How to start 'aedit'

  The program starts by the following operation:
          aedit[-a filename.aed] [-d|-n matrix_filename]

  '-a' indicates that an intial sequences are fetched from 'filename.aed'.
    Alignment sequence data file name should have '.aed'.

    This indication is optional, because user can load any file later.
  '-d'/'-n' indicates amino-acid/nucleic-acid sequence alignment modes.
    Without the indication, amino-acid mode works.
    Default font size, color and bar graph depends on the mode.
    User-defined matching index is fetched from 'matrix_filename'.
    The default matching index is Dayhoff's PAM250.

3.  Function of the program

  3.1  Top menu window

    Top menu window consists of seven sub-menus and two buttons.
    By clicking each submenu, a menu list comes in a pull-down manner.

    3.1.1  Sub-menu 'FIle'

      Open: a loading file can be selected by FileSelectionBox in OSF/Motif.

      Save: current data is saved into the indicated file.

      LogFile: logging a process while editing.

      Temporary: current alignment is automatically saved every five minutes.
                 The data is saved into 'temp_asd.aed'.
                 Also, manual saving is available:
                   Save(M.S.D.)     saves into 'temp_msd.aed'
                   Restore(M.S.D.)  restores from 'temp_msd.aed'
                   Restore(A.S.D.)  restores from 'temp_asd.aed'

    3.1.2  Sub-menu 'Edit'

      This menu doesn't work in View mode.

      Remove All Gap: removes all-gap columns.

      Clear: clears data.

    3.1.3  Sub-menu 'EditMode'

      View: editing is protected in this mode;
            clicking a character shows its residue number.

      Edit(Normal): gaps are inserted by clicking/dragging an area with the
                    left mouse button, and deleted by the middle mouse button.

      Edit(Constraint): not only gap insertion or deletion,
                        alignment constraints can also be defined by the right
                        mouse button.

      Amino(Insert): any characters can be inserted. (For a special use!)
				Operate like Emacs.

      Amino(Overwrite): any characters can be overwrited. (For a special use!)
				Operate like Emacs.

      Move(Alignment): the oder of sequences can be changed, by dragging
                       a sequence index with the left mouse botton.

      Alignment(Manual): the characters indicated with the left mouse botton
                         are forced to be aligned at the column indicated by
                         right mouse button clicking.

    3.1.4  Sub-menu 'MotifSearch'

      Motif patterns in Prosite database are searched in current alignment.
      No sequence motifs of RNA/DNA are contained.
      Homology threshold parcentage are defined with a scale widget;
        100% requires complete matching through motif-correspondent columns
      Searched motif patterns are shown in Prosite representation.
        By clicking each pattern, motif-correspondent columns turn grey.

    3.1.5  Sub-menu 'TreeDrawer'

      A phylogenetic tree based on the current alignment can be drawn
      by the mean distance method (UPGMA) or the nearest neighbour method.
      When the two trees are the almost same, the tree configuration is
      considered to be reliable.

      Exchange: The sequence order is changed according to the displayed tree.

    3.1.6  Sub-menu 'Alignment'

      A part of alignment is realigned automatically with PIM/UNIX.

      This menu works only in Edit(Constraint) mode, because constraints
        define the region to be aligned (3.2.3).

      Parameters UU(opening gapcost), VV(epxtending gapcost), SS(out-gap cost)
        and cut ratio are indicated with a scale widget just before running.

      PIM: don't operate while PIM is not available!!!!

        Tree-based:
             a quick alignment with tree-based construction.

        Tree-based Best-first Iterative:
             iterative best-first improvement
             after tree-based construction.

        Block-based:
             a quick alignment with tree-based construction, but
             subalignments in homologuous sequence sets are conserved.

        Block-based Best-first Iterative: 
             iterative best-first improvement
             after block-based construction.

        Best-first Iterative:
             iterative best-first improvement applied to the current alignment.

      UNIX:

        Tree-based:
             a quick alignment with tree-based construction.

        Tree-based Round-robin Iterative:
             iterative round-robin improvement
             after tree-based construction.

             Apply this to just a small alignment!!! Too much time!!

        Round-robin Iterative:
             iterative round-robin improvement applied to the current alignment.

             Apply this to just a small alignment!!! Too much time!!

    3.1.7  Sub-menu 'Options'

      Calc.ScoreTiming: When an alignment problem is so big that the responce
                        time is long enough to irritate, turn this mode to
                        Calc.WhenRefresh which reduces the score calculation
                        period to just when refreshing.

      AminoTextCase: switches characters uppercase/lowercase.

      Sorting: The sequence order is rearranged based on sequence similarity.
               SortInit: similarity is estimated by dynamic programming.
               SortNow: similarity is derived from the current alignment.

      IdenticalColumn: an identical character is displayed under each column.
               The identity threshold percentage can be definded.

      CostParameters: Default parameters can be changed.

      BarChart: MaxValue fixes the bar chart range and MotifRatio decides
                height of enlightened bars.

      Alarm Clock: an alignment is automatically saved every five minutes.
                   this changes the interval.

      Font: select a favorite font by clicking with the left mouse button.

      Color: character colors can be edit with this tool.
             SaveColor saves current color data to a file '*.clr'.
             LoadColor loads color data from a file '*.clr'.
             Background, FixColumn(3.2.2) and BarChart color can be changed.

    3.1.8  Button 'Refresh'

      Redraw the current display.

    3.1.9  Button 'Set'

      For constraint registration (3.2.3).

  3.2  Alignment editing

    3.2.0  How to scroll

      Horizontal column-to-column scroll:
		Clicking '<' or '>' at the ends of column number scale.

      Horizontal direct scroll:
		Clicking the scroll bar at the top right corner.

      Vertical scroll: NOT available!!!
		When aligning dozens of sequences, use tiny fonts.

    3.2.1  View mode (Default mode)

      No editing; Clicking a character have its residue number displayed.

    3.2.2  Edit(Normal) mode

      Gaps can be edited only by mouse operation.

      Inserting a gap: click location with the left button.
      Inserting a bunch of gaps: drag an area with the left button.
      Inserting a column of gaps: click just under the column
                                           with the left button.

      Deleting a gap: click a gap with the middle button.
      Deleting all gaps in an area: drag the area with the middle button.
      Deleting a column of gaps: click just under the column
                                           with the middle button.

      The operation described above with pressing right mouse button
	or Shift key, the left hand part of sequences moves.

      Fixing a column of alignment: to click just over the column
	on the number scale with the left button makes a column of alignment
	unchanged while	editing.  Click again to unfix.

    3.2.3  Edit(Constraint) mode

      Inserting a gap: click location with the left button.
      Inserting a bunch of gaps: drag an area with the left button.
      Inserting a column of gaps: click just under the column
                                           with the left button.

      Deleting a gap: click a gap with the middle button.
      Deleting all gaps in an area: drag the area with the middle button.
      Deleting a column of gaps: click just under the column
                                           with the middle button.

      The operation described above with pressing Shift key,
	the left hand part of sequences moves.

      CONSTRAINT-BASED AUTOMATIC ALIGNMENT
	This function makes it possible to align specific characters over
	a part of sequences automatically.

	1) Setting a number of constraints:
		i) Click/drag characters forced to be aligned
			with the right mouse button.
                        (Click/drag again to release.)
		ii) The high-lightened characters are registered as
			a constraint by clicking 'Set' button.
			More than two characters on the same sequence
			cannot be registered at a time.
                        (Click/drag again to release.)
		iii) Repeat i) and ii) a number of times.
	2) Setting a pair of column constraints:
		i) Click just under a column which is the end of region
			to be aligned. A column including any gaps is
			prohibited. Use the right mouse button.
                        (Click again to release.)
		ii) The high-lightened column is registered as
			a column constraint by clicking 'Set' button.
			Two columns cannot be registered at a time.
                        (Click again to release.)
		iii) Repeat i) and ii) once more.
	3) Indicating an alignment region:
		Click just over the region between the constrained columns.
		The corresponding part of number scale turns white.
	4) Executing an aligner:
		Choose an aligner with Sub-menu 'Alignment'.
		Set the alignment parameters.
		The alignment process on the indicated region starts
			when clicking 'OK'. Wait for a while!
	5) Result window comes up, when the execution ends.
		The result can be compared with the previous alignment.
		The result is replaced when clicking 'Embed'.

4.  Data file format

  See example files.
