>>>About seaview
Program seaview was published in:
Galtier, N., Gouy, M. & Gautier, C. (1996) SEAVIEW and PHYLO_WIN: two graphic 
tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci., 
12:543-548.

Seaview is available by anonymous FTP at pbil.univ-lyon1.fr in directory
/pub/mol_phylogeny/seaview for several unix platforms.

Seaview uses the Forms Library by T.C. Zhao and M. Overmars.
>>>Alignment panel
Mouse Use:

o Click on a site to position cursor (current cursor position -- sequence
  number, positions in alignment and in sequence -- appears at panel top center)
o Click on several sequence names to group them (names will appear in black
  background). Alignment operations (gap insertions/deletions) will operate on
  all grouped sequences simultaneously.
o Double-click on any name to group all sequences.
o Click with middle mouse button somewhere in sequence names to move grouped 
  sequences to another place in alignment.
o Click with right mouse button to deactivate the current grouping; all names
  return in normal print.

Active keys:

o The 4 keyboard arrows move the cursor
o > < move the view by 50 sites to right and left
o ] [ move the view by 5 sites to right and left
o - <space> insert a gap in the cursor sequence and members of its group if any
o <delete> or <backspace> delete a gap at left of cursor
o + inserts a gap in all sequences but that under the cursor and members of its
    group if any
o _ ("underscore") deletes a gap in all sequences but that under the cursor 
    and members of its group if any
o 1234567890 (digit keys) allow to compose a number (appearing under
  mult=number at top left of panel) used as a multiplier to an operation
  to follow (e.g., keys 4, 5, and - in sequence will insert 45 gaps)
o Alt+S (both keys together) save the alignment in the current filename using
  the current file saving format displayed by menu "Props". If format of 
  the last loaded file does not match the current saving format, this key
  is not active.

Mouse use on the site line (when there is one, white line at bottom):

Click with the left mouse button to select/unselect a site.
Drag the mouse with the left mouse button to extend or reduce a block of sites.
Click with the middle mouse button to extend the block of sites at left.
Click with the right mouse button on a block of sites to delete it.
>>>File menu
Open Mase, Open Phylip, Open Clustal, Open MSF, Open Fasta
               to load an alignment in one of these formats
               Mase format has the useful feature of allowing extra data beyond
               sequences and names (comments, accession numbers are
               really useful!). It can also store site sets [see
               item `Sites menu'].

<Alt>S Save    when active, saves the alignment in the current file (which
               name appears as window title), and indicates that keys
               <Alt> + S pressed together will perform this operation.

Save as...     allows to save the alignment under a filename to be chosen
               in the file selector appearing next [Pressing button Rescan
               therein may be necessary to have all files appear].

Save current sites
               only active when a site line is displayed; allows to save
               in a file only those sites of the sequences where an X is in the
               site line. If some sequences are selected, only these are saved.

Prepare printout
               Prepares a file adequate for alignment printout on a printer. The
               file selector appearing next allows to specify 3 parameters:
        block size     alignment lines may be divided in blocks (e.g. of size 10
                       for DNA/RNA sequences or 3 for protein coding sequences)
                       to ease alignment reading.
        chars/line     the max number of characters that fit on a printer line
                       (not the desired number of residues per line, which is
                       set to the largest fitting value by the program).
        lines/page     the number of lines that fit on a printer page (in order
                       that blocks of alignment lines are not divided by page
                       borders).

Quit           guess what?
>>>Props menu
Fontsize >   Tiny, Small, ..., Huge
             Sets the font size used to display sequences.

Save format> Save as Mase, as Phylip, as Clustal, as MSF, as Fasta
             Sets the file format used to save alignments
             [ `program resource' topic explains how to set default format]

Colors  >    DNA/RNA colors
             Forces sequences to be colored as DNA/RNA in case they were
             erroneously recognized as protein data.
        >    Protein colors
             Forces sequences to be colored as proteins in case they were
             erroneously recognized as DNA/RNA data.
        >    Alt. colors
             Uses alternate coloring rules defined for protein sequences
             [ `Program resources' topic below explains how to define them].
        >    Inverted colors
             Display residues as black letters on colored background instead
             of as colored letters on grey background.

Allow seq. edition
             When ON, residues can be deleted/inserted.
             when OFF (normally), only gaps can be deleted/inserted.

by Reference To display the alignment by reference to a particular sequence:
             residues identical to that of the ref. seq. are displayed as dots.
             Possible only when one sequence, the reference, is selected.
             Alignment edition is impossible while in the reference mode.
             When used, File:Prepare printout produces a printout by reference.
             Combination <Alt>+R is a shortcut for calling/exiting this mode.

DNA keys     Allows to use keys "hjkl" to enter DNA sequences
             "Allow seq. edition" should be ON for this item to be usable.
             Choose in the submenu what bases will be mapped to these keys 
        >    hjkl => GATC, hjkl => TCGA, hjkl => ACGT
             Also, the space bar will be mapped to base N.

Clustalw options
             Allows to specify options sent to the clustalw alignment program
             in order to set, e.g., specific alignement parameter values.
             Go to submenu "Edit options" and type desired options in the
             dialog window that appears. An example is to type /gapopen=5 
             When an option has been typed it is active unless you switch it off
             by calling again "Clustalw options" and sliding to the check box.
             Thus a set of options can be memorized and turned on and off.

Consensus option
             Allows to set the percent of identical residues needed to define
             a residue when building a consensus sequence. Sites where this
             fractions is not reached are filled with N or X.
>>>Sites menu
Site sets allow to specify parts of a multiple alignment to be retained for
further analyses (typically, those parts of the alignment taken as 
reliably aligned). Retained sites are depicted as series of Xs on a special 
line at bottom of the alignment panel. On color screens, they are also 
displayed by a dark background. Mouse clicks and drags on this line allow to
construct/alter the set.

Several sets of sites can be created and stored with the alignment if the Mase
format of alignment files is used. Each set has a name chosen by the user.
One set of sites at most can be displayed at any time through this menu.

Item "Save current sites" of menu "File" allows to save in an alignment
file only those sites of the alignment pertaining to the currently displayed
set. The resulting file may then be processed by, e.g., tree building
programs.

Create set      creates a line at bottom of alignment to hold the location
                of alignment sites.

Save set        stores changes done to the current set of sites

Rename set      stores the current set of sites under a new name

Hide set        hides (but remembers except unsaved changes) the current set of 
                sites

Delete set      removes the currently displayed set of sites from list of known
                sets

<name>          shows a sites line of name <name> constructed from data stored 
                in the alignment, or previously created
>>>Species menu
Species sets can be created and stored with the alignment if the Mase
format of alignment files is used.

To select one or several species, click or drag on their names; they will
appear in black background.

To memorize the current set of selected species, choose "Create set" from
this menu. The program will ask for a name for this set.

Delete set	deletes (just from memory) the current set of species.

<name>		Displays with black background the set of species memorized
		under that name.
>>>Footers menu
Comment lines can be created and displayed at bottom of the screen. These
lines can contain any text and the program will maintain the vertical
alignment between this text and sequences. This text can be saved using the
mase file format only.

To edit this text, click on the line name, position the cursor, and type text.
Click again on the line name to stop editing this text.

Show / Hide footers       To show / hide all footer lines

Create footer             To create a new footer line

Delete footer             To delete the currently selected footer line


>>>Search button & box
Type a string in box at right and strike <return> key or push button to
position the cursor in the next occurence of this string from its current
place.

Push button to position the cursor at next occurence of the current
search string.

Sequence gaps are ignored by the search procedure.
>>>Goto button & box

           Moves the cursor to desired position or sequence

Position:
Type a number in box at right and hit <return> key or push button to
position the cursor at that position of the alignment.

Sequence:
Type a (fragment of) sequence name in box at right and hit <return> key or 
push button to position the cursor in that sequence. Case is not significant.
>>>Edit menu
Rename sequence          To rename the currently selected (= name in black 
                         background) sequence.

Edit comments            To see or change comments of the currently selected
                         sequence (Comments can only be saved in mase format).

Delete sequence(s)       Deletes all selected sequences from the alignment.

Create sequence          Allows to create a new-empty sequence in the alignment;
                         set "Allow seq. edition" from "Props" menu ON 
                         to be able to type the sequence in.

Load sequence            Allows to load a new sequence in the alignment.
                         The sequence can be typed in or pasted from a
                         selection made in another window: drag on the
                         sequence data, and paste it with the middle mouse 
                         button in the `Sequence loading' window.

Duplicate sequence       Allows to duplicate the currently selected sequence
                         wih prefix D_ in its name.

Complement sequence      Creates a new sequence equal to the complementary 
                         strand of the currently selected sequence with prefix 
                         C_ in its name.

Reverse sequence         Creates a new sequence by reading 3' -> 5' the 
                         currently selected sequence and named with prefix R_

Exchange Us and Ts       Exchange bases Us and Ts in all currently selected 
                         sequences.

Align sites              Runs the clustalw alignment program on the block of 
                         selected sites and the set of selected sequences.

Dot plot                 Performs a "dot plot" analysis of the two selected 
                         sequences. See "Dot plot" item of the help data.

Consensus sequence       Computes the consensus of all currently selected
                         sequences. At any site, the consensus residue is the
                         most frequent one if its frequency is above a threshold
                         value. This threshold (60 % by default) can be changed
                         through item "Consensus threshold" of menu "Props".
                         Below threshold, N or X is used.
>>>Dot plot
              Performs a "dot plot" analysis of two sequences

Enter desired values for the window size and # of matches/window, and click
on button "Compute", the dot plot will appear.

Click in the dot plot, the corresponding sequence regions appear in
the alignment panel above the dot plot. Use "Magnify" to take a close look.
Click on arrows at left to move the hit point by one residue in either of
six directions.
Move the slider below the alignment panel to control the number of displayed
residues.

Fit to window, Reduce, Magnify: perform zoom in and out operations
Write Postcript: saves the dot plot in a file called from the alignment name
                 with extension .ps
Close: closes the dot plot window

                   To perform a dot plot-guided alignment
                   --------------------------------------
Click on a diagonal representing two sequence parts to be aligned, then click
on button "align".
Repeat this for each sequence parts you want to be aligned to each other.
To transfer into the multiple alignment the result of these operations, click on
button "Record alignment".
Most often, one of the two compared sequences is already aligned to other
sequences of the multiple alignment, while the other one is not. Choose which
of the two sequences is already aligned by clicking on the arrow next to
"Ref. sequence".
>>>Mase file format
Mase files follow the following format:

Zero or more header lines each beginning with ;;
Next, for each sequence in the alignment:
One or more comment lines each beginning with ;
Sequence name alone on a line (may be long and may contain spaces)
Sequence data in free form, possibly with numbers and spaces ignored while 
reading the file. Dashes denote gaps.

Header lines may contain any text and also contain descriptions of site sets and
of species groups when such data have been defined.

Site sets are written as in this example:
;;# of segments=10  mychoice
;; 14,74 221,256 416,449 990,1148 1363,1384 1474,1483 1556,1668 2034,2062
;; 2114,2139 2756,2859
where "mychoice" is the name of the set of sites and where the series of pairs
of numbers lists the endpoints of successive block of sites.

Species groups are written as in this example:
;;@ of species = 4 distant outgroup
;; 2, 3, 4, 5
where "distant outgroup" is the name of the species group and where the series
of numbers lists the ranks of sequences members of the species group.
>>>Program arguments
Program is run by command
seaview [options] [filename]

where options may be
-save <format_name>
         [format_name, either  mase, clustal, phylip, msf, or fasta sets the 
          default file format for saving operations]
-fast
         [sequences will be displayed faster but less smoothly]
-reducefonts
         [may be necessary on 100dpi displays if some fonts are too big]
-inverted
         [residues will appear as black letters on a colored background]

and filename 
is an optional alignment file to be loaded. The expected format for this file
is that of the default format for saving operations.

See `Program resources' topic to know how to further customize the program.
>>>Program resources
Several X resources allow to customize the program.

                       MISCELLANEOUS SETTINGS

          | Resources -->
----------|-------------------------------------------------------------------
Purpose   | default | name of      | fast but | reduce fonts| residues shown |
          | saving  | help file    | rough    | on 100dpi   | on colored     |
          | format  |              | display  | screens     | background     |
----------|-------------------------------------------------------------------
Name      | save    | helpfile     | fast     | reducefonts | inverted       |
----------|-------------------------------------------------------------------
Type      | string  | string       | boolean  | boolean     | boolean        |
----------|-------------------------------------------------------------------
Def. value| mase    | seaview.help | False    | False       | False          |
----------|-------------------------------------------------------------------
Example   | clustal | seaview.aide | True     | True        | True           |
----------|-------------------------------------------------------------------

Notes: 
1) Known file formats are mase, clustal, phylip, msf, fasta.
2) The help file is sought in all directories listed in the PATH variable.
================================================================================

     SETTING GROUPS OF AMINO ACIDS DISPLAYED WITH THE SAME COLOR

          | Resources -->
----------|---------------------------------------------------------
Purpose   | standard coloring         | alternate coloring         |
          | of aminoacids             | of aminoacids              |
----------|---------------------------------------------------------
Name      | stdcolorgroups            | altcolorgroups             |
----------|---------------------------------------------------------
Type      | string                    | string                     |
----------|---------------------------------------------------------
Def. value| EDQNHRKBZ,ILMV,APSGT,FY,WC| none                       |
----------|---------------------------------------------------------
Example   | DEBZ,ACWY,FGHIK,LMNPQRSTV | ILMV,ACGPST,DENQBZ,HKR,FWY | 
----------|---------------------------------------------------------

Note: Default colors are red, green, yellow, blue, violet, pink, black, gold, 
and orange. These can be changed (see below).
White is used for gaps and for unlisted residues.
The above 2 resources allow to set which aminoacids will be painted in what
of the above colors. The format for these resources is, e.g.,
EDQNHRKBZ,ILMV,APSGT,FY,WC
to specify
aminoacids | EDQNHRKBZ | ILMV  |  APSGT |  FY  |   WC   | others + gaps |
color      |    red    | green | yellow | blue | violet |   white       |
The number of listed groups of aminoacids determines the number of colors used.
================================================================================

                 CHANGING COLORS USED TO DISPLAY SEQUENCES

          | Resources -->
----------|---------------------------------------------------------------------
Purpose   | set DNA colors           | set protein colors                      |
----------|---------------------------------------------------------------------
Name      | dnacolornames            | protcolornames                          |
----------|---------------------------------------------------------------------
Type      | string                   | string                                  |
----------|---------------------------------------------------------------------
Def. value| red,green,yellow,blue    | red,green,yellow,blue,violet,pink,black,|
          |                          |                              gold,orange|
----------|---------------------------------------------------------------------
Example   | blue,yellow,255 0 0,green| salmon,154 255 154,lightyellow2,lavender|
----------|---------------------------------------------------------------------
Notes:
Colors are defined either by a name from your rgb.txt file  
                       or by 3 RGB numbers.
For DNA/RNA, the 4 listed colors apply to A, C, G, and T/U, respectively.
For proteins, at most 9 color names can be listed.
================================================================================

                     CONTROLING PRINTOUT OPERATION

          | Resources -->
----------|--------------------------------------------------------------
Purpose   | blocksize for      | chars/line for    | lines/page for     |
          | printout operation | printout operation| printout operation |
----------|--------------------------------------------------------------
Name      | printoutblock      | printoutcpl       | printoutlpp        |
----------|--------------------------------------------------------------
Type      | integer            | integer           | integer            |
----------|--------------------------------------------------------------
Def. value| 10                 | 80                | 60                 |
----------|--------------------------------------------------------------
Example   | 3                  | 90                | 60                 |
----------|--------------------------------------------------------------
>>>Setting resources
Each resource is specified by a line of the form
Seaview*<resource-name>:	<resource-value>

Examples:
Seaview*dnacolornames:		blue,yellow,green,255 0 0
Seaview*altcolorgroups:		AC,DEFGHIK,LMNPQRS,WY,TV
Seaview*save:			clustal
Seaview*printoutcpl:		90
Seaview*inverted:		True
Seaview*reducefonts:		True

Resource lines are added by any of 4 means:
1) in a file called Seaview in directory /usr/lib/X11/app-defaults
2) in a file called Seaview in any directory pointed to by environment variable
XAPPLRESDIR
3) in your ~.Xdefaults file
4) interactively loaded by command
xrdb -merge fname
where "fname" is a file containing resource lines
and checked by command
xrdb -query
>>>To reduce button labels
On 100 dpi screens, button labels and other components may be too big.
To repair that use the following 3 resources:
Seaview*buttonFontSize: 8
Seaview*menuFontSize: 	8
Seaview*reducefonts: 	True

Topic 'Setting resources' above explains where to place these resources.