Program seaview was published in:
Gouy, M. Guindon, S. & Gascuel., O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224.
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.

Version 4.2.12

Binaries and full source code available from http://pbil.univ-lyon1.fr/software/seaview.html

(C) 1996-2009 Manolo Gouy
Laboratoire de Biometrie et Biologie Evolutive
CNRS / Universite Lyon I

Licensed under the GNU General Public Licence (http://www.gnu.org/licenses/gpl.txt)

Seaview drives the Muscle, ClustalW2 and PhyML programs and uses code from the PHYLIP package for parsimony. Please quote:

• Edgar R.C. (2004) "MUSCLE: multiple sequence alignment with high accuracy and high throughput." Nucleic Acids Res. 32(5):1792-1797.
• Larkin M.A. et al. (2007) "Clustal W and Clustal X version 2.0." Bioinformatics 23(21) 2947-2948.
• Guindon S., Gascuel O. (2003) "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood." Systematic Biology 52(5):696-704.
• Felsenstein J. (1993) PHYLIP version 3.5.

Some seaview versions use the PDFlib Lite library (http://www.pdflib.com) for pdf output under the "Open Source Developer Exemption" of the PDFlib Lite License Agreement.

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 select them (names will appear in black background). Alignment operations (gap insertions/deletions) will operate on all selected sequences simultaneously.
• Click with middle mouse button or Ctrl-Click somewhere in sequence names to move selected sequences to another place in alignment.
• Click with right mouse button or Shift-Click to deactivate the current selection.
• Cmd-Click(Mac), Alt-Click(PC), or Ctrl-Click (unix) on sequence name to select from last selected sequence to here.

• The 4 keyboard arrows move the cursor. Page up/down keys move it one pageful.
• > < move the view by 50 sites to right and left (other keys can be used)
• ] [ 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
• - or <space> insert a gap in the cursor sequence and members of its group if any
• <delete> or <backspace> 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)
• ctrl/cmd+S (according to platform) saves the alignment in the current filename using its current format.

• Click mouse to select/unselect a site.
• Drag with the mouse button an extremity of a block of sites to extend or reduce it.
• Click with the middle mouse button or Ctrl-Click to extend the block of sites at left.
• Click with the right mouse button or Shift-Click on a block of sites to delete it.

Open, Open Mase, Open Phylip, Open Clustal, Open MSF, Open Fasta, Open NEXUS: to load an alignment in one of these formats. Formats Phylip, Clustal and Fasta use _ instead of space in names. Only the interleaved version of the Phylip format is supported. 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 trees, site sets [see Sites Menu], species sets, footers, genetic code information.

Import from DBs: to import one or several sequences from databases (EMBL, GenBank, SwissProt/UniProt) into the alignment window naming them either by their ID or LOCUS record name or by their species. Sequences can be identified by two means:
1. By name, accession number or keyword. Protein IDs, without their extension (e.g., CAA06608 from /protein_id="CAA06608.1"), are processed as keywords attached to sequences, so can also be used. Because imported sequences are named with information taken from their ID/LOCUS record, the protein ID won't be used to name the sequence.
2. By a local text file of names or accession nos (one per line, strict text file, e.g., not a .doc or .odt file).
In case 1. and for nucleotide databases, it is also possible to import sequence fragments corresponding to a specified feature key (e.g., CDS, rRNA, tRNA) and, optionally, to require a given string to be present in the feature's annotations. If no matching string is specified, only the first matching feature key is imported. CDSs are imported with their correct genetic code and reading frame. Imports require an internet connection that allows outbound access to port # 5558. Access to a series of other databases is also possible.

Save: when active, saves the alignment in the current file (which name appears as window title). The shortcut for this operation is Ctrl-S (Cmd-S on Mac).

Save as...: to save the alignment under a name and a format to be chosen in the file selector appearing next.

Save selection: only active when some sequences are selected or when a site line is displayed; allows to save in a file selected sites, or selected sequences, or selected sites of selected sequences.

Save prot alignmnt: only active when a nucleotide alignment is translated to proteins; allows to save resulting protein sequences in any format.

Prepare pdf: Writes the alignment as a pdf file with optional choices set through the File/pdf options menu item or the file dialog on Mac OS:

• fontsize: sets the fontsize (font is Courier)
• block size: alignment lines may be divided in blocks (e.g., of size 10 for DNA/RNA sequences or 3 for protein coding sequences) separated by one space to ease alignment reading.
• paper size: two paper formats can be used A4 or LETTER
• color/B&W: choose between colored alignment or one with all black letters.
• variable sites only: available only in reference mode, allows to output only variable sites of the alignment and their positions.

Concatenate: To add one alignment (source) to the end of another (target). Can be done "by name" (seqs with same name are concatenated) or "by rank" (seqs with same rank in alignments are concatenated). Option "add gaps" replaces names absent in either alignment by gap-only sequences ("by name" only).

New window: Opens a new, empty alignment window.

Close window: Closes the alignment window.

Quit: guess what?

Copy selected seqs: only active when some sequences are selected; copies in clipboard these sequences, or only their selected sites if a site line is displayed.
Paste alignment data: To paste previously copied alignment data to the end of the current alignment window.
Select all: Selects all sequences from the alignment.
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 formats).
Edit sequence: To edit the selected sequence, typically by pasting external data, or by opening two edit sequence windows and transferring sequence data between them.
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.
Duplicate sequence: Duplicates the currently selected sequence with 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.
Dot plot: Performs a dot plot analysis of the two selected sequences.
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 options> Edit threshold" of menu Props. Below threshold, N or X is used.
Del gap-only sites: Deletes all gap-only sites from the alignment.
Set genetic code: Allows to specify the genetic code used to translate to protein the selected sequence(s). Active only with nucleotide alignments. Genetic codes are saved if the mase or NEXUS file formats are used.

Align all
Align selected sequences: Runs the chosen alignment program on all or on selected sequences. Alignment program is chosen with Alignment options of menu Align. With MSWindows and Unix, the chosen alignment program is searched in the directory of the seaview program and in directories of your PATH.
Align selected sites: Runs the chosen 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 alignment in the chosen sequence will be preserved in the new alignment.
Profile alignment: Align selected sequences against a profile, that is, a group of pre-aligned sequences.
Possible operations for making a profile alignment:

1. select members of the profile group;
2. do 'Create group' of menu Species;
3. select sequences you want to align against the profile group;
4. do 'Profile alignment' of menu Align;
5. choose the profile group in the dialog menu;
6. choose alignment algorithm;
7. if using clustalw2, choose between "each sequence to profile" and "profile to profile" (with "profile to profile", selected sequences are expected to be pre-aligned to each other). With clustalw2, option Quicktree is possible.
8. Uncheck "Propagate gaps to sites" if you don't want gaps created in the profile group by the profile alignment to be propagated to all your site selections (menu "Sites").

• clustalw2, muscle, ...: Allows to choose the desired alignment method.
• Edit options: Without options, the algorithm's default parameter settings, adequate for many problems, are used. This item allows to define custom alignment parameter settings by listing a series of options (e.g., -quicktree -gapopen=5 for clustalw2) that will be transmitted to the alignment algorithm.
  • clustalw2 options are fully described in clustalw_help.txt.
  • Muscle options are fully described in Muscle command line reference.
  Options are active unless you switch them off by unchecking the check box. Thus a set of options can be memorized and turned on and off.
• Add external method: Interfaces seaview with an external multiple sequence alignment method. Any external alignment program able to read a fasta file and output a fasta file and that can be run by a 'name + arguments' command line is usable. Select the external program from your computer or enter its name. Under MSWindows and Unix, the name is searched in seaview's directory and in all PATH directories. Under Mac OS, the name is searched in all PATH directories, and in directory <seaview-bundle>/Contents/Resources. Enter its arguments replacing the method's input and output filenames by %f.pir and %f.out, respectively. The yellow tip message that appears when the mouse remains on the "Arguments" field gives two examples of external program interfacing. Standard output redirection to a file with > is possible.
• Delete method: To delete currently selected alignment method. clustalw2 and muscle can't be deleted.

Fontsize: 8, 10, ..., 36: Sets the font size used to display sequences.
View as proteins: When ON, DNA sequences are displayed as translated to protein sequences. This allows to align them, and to go back to the DNA level by unselecting this item. Items Save/Save as of menu File and sequence edition are impossible when ON.
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 [see Sequence coloring help topic].
• Codon colors: Each codon gets colored according to its corresponding aminoacid.
• Inverted colors: Display residues as black letters on colored background instead of as colored letters on grey background.

Site sets allow to specify parts of a multiple alignment to be retained for further analyses (e.g., 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. Mouse clicks and drags on this line allow to construct/alter the set (see Mouse use on the site line).

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 selection of menu "File" allows to save in an alignment file only those sites of the alignment pertaining to the currently displayed site set.

Create set: creates and names a new site set and displays it at bottom of alignment. A custom site set or, for nucleotide sequences, one of four codon position masks, or the set of all variable sites, can be created. Custom site sets are initially defined to contain all alignment sites, and should be named by the user. Codon position masks and the variable sites set are precomputed and named by the program. They are better used once alignment operations are completed.
Duplicate set: duplicates the current set of sites under a new name
Hide set: hides (but remembers) the current set of sites
Delete set: removes the currently displayed set of sites from list of known sets
name: shows the site line of name name. It can have been read in together with the alignment data, or previously created by "Create set".

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.
name: displays with black background the set of species memorized under that name.

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

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.

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.

This menu allows to compute, draw, save, and import DNA or protein phylogenetic trees.
Protein-coding DNA sequences displayed as protein sequences (item "View as proteins" of menu Props) are treated as protein sequences.
All tree computations apply to selected sequences (or all if none) and selected sites (or complete alignment if none).
All trees, sequence, and site selections can be saved together with the alignment data in either the mase or Nexus formats.

Parsimony:
Computes parsimony trees using PHYLIP's v3.52 dnapars or protpars programs and returns the strict consensus of all equally parsimonious trees found, without branch lengths.
Randomize seq. order: to repeat search for shortest trees with randomized sequence order.
Ignore all gap sites: if on, all gap-containing sites are excluded from analysis.
Gaps as unknown states: if on, gap-containing sites are coded as unknown states so don't introduce parsimony steps; if off, they are treated as an additional character state. The interface forbids the meaningless configuration that would ignore gaps and treat them as unknown states.
Equally best trees retained: maximum number of equally best trees retained in search.
Bootstrap: performs bootstrap evaluation of clade statistical support (can be interrupted).
User tree: computes the number of steps of a user-given tree taken from those in the trees menu. Such trees can have been previously computed or imported from external source.

Distance methods:
Computes NJ or BioNJ trees on a variety of pairwise phylogenetic distances.
NJ/BioNJ: to select the tree-building algorithm
Save to file: does not compute any tree but saves sequence pairwise distances to a local file.
Distance: select one among a variety of evolutionary distances: J-C: Jukes & Cantor (1969); K2P: Kimura (1980) JME 16:111; HKY: Rhzetsky & Nei (1995) MBE 12:131; LogDet: Lake (1994) PNAS 91:1455; Lockhart et al. (1994) MBE 11:605; Ka/Ks: Li (1993) JME 36:96.
ignore all gap sites: if on, all gap-containing sites are excluded from analysis; if off, not all sequence pairs use the same set of sites for computation of distances.
Bootstrap: performs bootstrap evaluation of clade statistical support (can be interrupted).
User tree: computes least squares branch lengths for selected user tree topology.

PhyML:
Computes trees using PhyML v3.0.1 as an external program.
If needed, PhyML can be downloaded from http://www.atgc-montpellier.fr/phyml/binaries.php
Under Unix, file $HOME/.seaviewrc may contain the name of the PhyML executable used by seaview.
Please quote: Guindon S, Gascuel O. (2003) "A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood." Systematic Biology 52(5):696-704.
Model: select one among a variety of evolutionary models.
Branch support: can be omitted (None) or estimated either by the approximate likelihood ratio test approach (aLRT) or by bootstrap.
Ts/Tv ratio: (applies to some nucleotide models only) optimize or fix a priori this ratio.
Invariable sites: ignore (None), optimize, or set to an a priori value (Fixed) the fraction of invariable sites.
Across site rate variation: ignore (None), optimize, or set to an a priori value (Fixed) the alpha parameter of the gamma distribution of rates across sites. If not ignored, the # of rate categories must also be set.
Tree searching operations: NNI (nearest-neighbor interchange), SPR (subtree pruning and regrafting) and 'best of NNI & SPR' are options improving the search for the most likely tree but requiring increasing computation time.
Starting tree: controls the tree used to start tree-space search; can be BioNJ, a user-given tree from the trees menu, or a number of random trees (possible only with SPR). Turn off "Optimize tree topology" to compute the likelihood of a user-given tree.

Import tree: to import an external, Newick-formatted tree.

New tree window: opens a new, empty tree window.

File menu

Save to Trees menu: to save in menu Trees of alignment window a previously computed tree.
Remove from Trees menu: removes a tree from menu Trees of alignment window.
Save rooted (unrooted) (sub)tree: saves displayed tree or subtree to a local file as rooted or unrooted form.
Print: (Mac OS and MSWindows only) prints displayed tree (see also 'Page count' below).
Save as PDF/PostScript: saves displayed tree to PDF (or PostScript) local file (see Page Count).
A4 - Letter: controls the page format for PDF/PostScript operations.
Page count>#: controls the # of pages used for print/PDF/PostScript operations.
Reorder following tree: reorders sequences of alignment window as in displayed tree.
Select in alignment: selects in alignment window all members of subtree (active when only a subtree is plotted).
Open tree or alignement: opens a new tree (Newick format) or alignment file (any format).
New window: opens a new, empty tree window where a Newick-formatted tree can be pasted from clipboard.
Close window: closes the displayed tree that gets lost unless it had been saved to Trees menu.

Edit menu

Copy: (Mac OS and MSWindows only) copies tree plot to clipboard for pasting to external programs.
Paste tree: to paste a Newick-formatted tree contained in the clipboard (only if window is empty).
Find: finds sequence names in tree that contain a user-given string, and red-colors them in tree display (case insensitive).
Again: repeats 'Find' operation with same matching rules.
Edit tree header: to change the tree's brief descriptive header line.
Bootstrap threshold: only bootstrap values above given threshold become displayed.
Root at tree center: roots the tree at its point most equidistant to all leaves (when branch lengths exist).
Get or Set window size: to control the size of the current tree window.
Edit tree shape: to alter tree shape by moving or deleting sequence groups. A new window displays the tree without branch lengths. Clicking on a square selects a sequence group that appears in red. It can be moved to another branch of tree by clicking on another square, or deleted ("Delete group" button). "Select group" button allows to select another group for further move or delete operations. Complete edits by pressing "End edit" button, and, possibly, "File/Save to Trees menu".

Font menu: to control font, style and size of all text in tree display.

Br lengths: toggles display of branch length values next to each branch (very small values are not displayed).
Bootstrap: toggles display of bootstrap (or aLRT) support value next to each branch.

squared/circular/cladogram: toggles display between squared plot convenient for rooted trees, circular plot convenient for unrooted trees, and cladogram which displays trees with all branch lengths a multiple of a unit length and all leaves aligned at right. Cladogram is not available for branch length-free trees because it is equivalent to the squared display for them.

Full: normal, full tree display.
Swap: to swap branches around a node. Click on relevant square that appears.
Re-root: to set tree outgroup. Click on relevant square that appears.
Subtree: to limit display to a subtree. Click on relevant square that appears.
Subtree up: when a subtree is being displayed, adds one more node towards tree root to display.

Zoom: vertical zoom for tree display; one or two scrollers appear. The tree can be moved by the scrollers, the mouse wheel, or by clicking on and dragging the plot.

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 displayedresidues.

Fit to window, Reduce, Magnify: perform zoom in and out operations
Write PDF/ps: saves the dot plot to a PDF or PostScript file.
Close: closes the dot plot window

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 trees, site sets and species groups when such data have been defined.

Trees are as in this example:

;;$ BioNJ tree
;;[BioNJ 658 sites J-C](((boli_haplo_03:0.00146,boli_haplo_06:0.00159):0.00159,bol
;;i_haplo_05:0.00146):0.02886,boli_haplo_01:0.03142);

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

Species groups are written as in this example:

;;@ of species = 4 distant outgroup
;; 2, 3, 4, 5

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]
-fontsize n
         [sets to integer n the initial fontsize of the alignment panel]

and filename 
is an optional alignment file to be loaded. 

Use item "Customize" of menu Props to further customize the program.

catalog of amino acid colors: colors used for each amino acid family. Click on any to control the desired shade, as explained above. White is used for gaps and for unlisted residues.

Example: with the default coloring scheme, groups of amino acids KR and AFILMVW are displayed with the first and second catalog colors, respectively.

Click "reset" to use default amino acid families and color catalog. "Apply" or "Set changes permanent" to apply new shades to current alignment.

• [sites] background grey: move the slider to change the grey shade of the alignment panel background; the "sites" shade applies to selected sites only; "reset" gives default values to both shades.
• right-left movement keys: define 4 keys that move cursor right and left by 5 or 50 residues; reset uses default keys.
• display lowercase: select so that lowercase characters present in sequence data are not displayed as uppercase.
• inverted: select to display sequences as black letters on colored background.
• spaces in FASTA names: If on, all characters after the '>' will be interpreted as sequence name in FASTA files. If off, the name ends at the first encountered space and the rest of the line (if any, e.g., length information) is interpreted as sequence annotation data.
• alignment algorithm: to set the default alignment algorithm used by menu Align.
• default save format: sets the default format of the "File:save as" menu item.
• pdf page, pdf fontsize: sets the page format and font size used by item "Prepare pdf" of menu File.
• max name width: the maximum width at which sequence names are displayed; names longer than that are accepted but aren't entirely displayed.
• phylip names width: sequence names longer than this value are truncated when saving PHYLIP-formatted alignments. Value 10 should be used to interface with the PHYLIP package. Larger values are more convenient for, e.g., PhyML, PAML.

• Mac OS: Custom settings are stored in file fr.cnrs.seaview.plist of the user's Library/Preferences folder.
• MSWindows: Custom settings are stored in file seaview.ini in the same directory as seaview program.
• Unix: Custom settings are stored in file .seaviewrc in the user's home directory.