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Seaview Manual
About seaview
Program seaview was published in:
Galtier, N., Gouy, M. and 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 and for Windows95/98.
Seaview uses the FLTK library by Bill Spitzak and others.
Alignment panel
Mouse Use:
- Click on a site to position cursor (current cursor position -- sequence number, positions in alignment and in sequence -- appears at panel top center)
- Click or drag mouse 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.
- Double-click on any name to group all sequences.
Ctrl-Click somewhere in sequence names to move grouped sequences to another place in alignment. - Shift-Click to deactivate the current grouping; names return in normal print.
- Click with middle mouse button somewhere in sequence names to move grouped sequences to another place in alignment.
- Click with right mouse button to deactivate the current grouping; all names return in normal print.
Active keys:
- The 4 keyboard arrows move the cursor
- > < move the view by 50 sites to right and left (other keys can be used)
- o ] [ move the view by 5 sites to right and left (other keys can be used) see "Miscellaneous options" for how to use other keys for same purpose
- - insert a gap in the cursor sequence and members of its group if any
- or delete a gap at left of cursor
- + inserts a gap in all sequences but that under the cursor and members of its group if any
- _ ("underscore") deletes a gap in all sequences but that under the cursor and members of its group if any
- 1234567890 (digit keys) allow to compose a number (appearing under mult=number at bottom left of panel) used as a multiplier to an operation to follow (e.g., keys 4, 5, and - in sequence will insert 45 gaps)
- 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 mouse to select/unselect a site.
- Drag with the mouse button an extremity of a block of sites to extend or reduce it.
- Ctrl-Click to extend the block of sites at left.
- Shift-Click on a block of sites to delete it.
- Click with the left mouse button to select/unselect a site.
- Drag with the left mouse button an extremity of a block of sites to extend or reduce it.
- 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, Open NEXUS
to load an alignment in one of these formats.
Mase and Nexus formats have the useful feature of allowing extra data beyond sequences and names (comments, accession numbers are really useful!). They can also store site sets [see item `Sites menu'].
S Save
when active, saves the alignment in the current file (which name appears as window title), and indicates that keys + 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, as NEXUS
Sets the file format used to save alignments [`Miscellaneous options' 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.
Colors > Protein colors
Forces sequences to be colored as proteins in case they were erroneously recognized as DNA/RNA data.
Colors > Alt. colors
Uses alternate coloring rules defined for protein sequences [`Coloring schemes' topic below explains how to define them].
Colors > 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 +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
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 fraction is not reached are filled with N or X.
Fast-Rough
Allows to switch between smooth-slow or rough-fast display.
Allow lowercase
If set, lowercase residues will be apparent. If not set, lowercase residues in sequence files display as uppercase.
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 or NEXUS formats of alignment files are 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
- shows a sites line of name constructed from data stores in the alignment, or previously created
Species menu
Species sets can be created and stored with the alignment if the Mase or NEXUS formats of alignment files are 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.
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 or NEXUS file formats 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 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 and box
Moves the cursor to desired position or sequence
Position:
Type a number in box at right and hit 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 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/NEXUS).
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. A window will ask for choosing the reference sequence: gaps present before clustalw alignment in the chosen sequence will be preserved in the new alignment.
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
#ifdef WIN32
Arguments can be used to associate files with the seaview program.
#endif
Program is run by command
seaview [options] [filename]
where options may be
-save
[format_name, either mase, clustal, phylip, msf, nexus or fasta sets the initial file format for saving operations and for opening the file given on command line; default is mase]
-fast
[sequences will be displayed faster but less smoothly]
-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 customization' topic to know how to further customize the program.
Program customization
Seaview can be customized through several options to be put in a text file called "seaview.ini" located in the same directory as program seaview itself.
Next help items describe all these options.
Each option is specified by a line in this file of the form =
stdcolorgroups = AC,DEFGHIK,LMNPQRS,WY,TV
save = clustal
printoutcpl = 90
inverted = True
#else
Seaview can be customized by several options specified as program resources.
Next help items describe all these options.
Each resource is specified by a line of the form Seaview.:
Seaview.dnacolors: blue,yellow,green,255 0 0
Seaview.altcolorgroups: AC,DEFGHIK,LMNPQRS,WY,TV
Seaview.save: clustal
Seaview.printoutcpl: 90
Seaview.inverted: 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 $HOME/.Xdefaults file
(note that this is effective only if this file is read by your login procedure)
4) interactively loaded by command
xrdb -merge fname
where "fname" is a file containing resource lines and checked by command
xrdb -query
Miscellaneous options
See 'Program customization' topic for how to set these options.
MISCELLANEOUS OPTIONS
Purpose (note)| Name | Default value | Example of possible value
---------------------|-----------|---------------|-----------------------------
saving format (1)| save | mase | clustal
name of help file (2)| helpfile | seaview.hlp | seaview.aide
name of help file (2)| helpfile | seaview.help | seaview.aide
fast, rough display | fast | false | true
colored background | inverted | false | True
keys to move view | movekeys | ][>< | }{.,
allow lowercase | lowercase | false | TRUE
window size | window | 900x550 | 800x400
window size | window | 1000x700 | 800x400
emul. 3-button mouse |emulate_3_b| false | True
(3)| | |
Notes:
1) Possible file formats are mase, clustal, phylip, msf, fasta, nexus.
2) The help file is sought in the directory containing program seaview.
3) The help file is sought in all directories listed in the PATH variable
and in the current directory.
4) if yes, use CTRL-click for middle button & SHIFT-click for right button
Coloring schemes
See 'Program customization' topic for how to set these options.
SETTING GROUPS OF AMINO ACIDS DISPLAYED WITH THE SAME COLOR
By default, amino acids are split in 5 families each displayed in a different
color. These families can be customized, up to a maximum of 10 families. Also, an alternative coloring scheme can be defined, and seaview will allow to switch between the first and the alternative coloring schemes.
Purpose | Name | Default value | Example of value
--------------------|----------------|-----------------|-----------------
standard coloring | stdcolorgroups | EDQNHRKBZ,ILMV, | DEBZ,ACWY,FGH
scheme of aminoacids| | APSGT,FY,WC | IK,LMNPQRSTV
| | |
alternate coloring | altcolorgroups | | ILMV,ACGPST,DEN
scheme of aminoacids| | | QBZ,HKR,FWY
Note: Default colors are red, green, yellow, blue, cyan, magenta, salmon, purple, aquamarine, and dark-gray. These can be changed (see 'Defining colors').
White is used for gaps and for unlisted residues.
The above 2 options allow to set which aminoacids will be painted in what of the above colors. The format for these is, e.g., EDQNHRKBZ,ILMV,APSGT,FY,WC to specify
aminoacids | EDQNHRKBZ | ILMV | APSGT | FY | WC | others + gaps |
color | red | green | yellow | blue | cyan | white |
The number of listed groups of aminoacids determines the number of colors used.
Defining colors
See 'Program customization' topic for how to set these options.
CHANGING COLORS USED TO DISPLAY SEQUENCES
Purpose | Name | Default value | Example of value
----------------|------------|----------------------------|---------------------
set DNA colors | dnacolors | red,green,yellow,blue | 100 0 0,0 100 0,0 0
| | | 100,100 100 0
| | |
set prot. colors| protcolors | red,green,yellow,blue, | 100 0 0,0 100 0,
| | cyan,magenta,salmon,purple,| 0 0 100,100 100 0,
| | aquamarine,dark-gray | 0 100 100,100 0 100
set DNA colors | dnacolors | red,green,yellow,blue | blue,yellow,255 0 0,
| | | green
| | |
set prot. colors| protcolors | red,green,yellow,blue, | salmon,154 255 154,
| | cyan,magenta,salmon,purple,| lightyellow,lavender
| | aquamarine,dark-gray |
Notes:
Colors are defined by 3 RGB numbers in range 0-255.
Colors are defined either by a name from your rgb.txt file or by 3 RGB numbers in range 0-255.
For DNA/RNA, the 4 listed colors apply to A, C, G, and T/U, respectively.
For proteins, at most 10 colors can be listed.
Printout options
See 'Program customization' topic for how to set these options.
CONTROLING PRINTOUT OPERATION
Purpose | Name | Default value | Example of possible value
--------------|---------------|---------------|--------------------------
block size | printoutblock | 10 | 3
chars/line | printoutcpl | 80 | 90
lines/page | printoutlpp | 66 | 60
Note: the value of printoutcpl stands for the full page width.
