| ## EMBOSS: showalign

# Program showalign

## Function

Displays a multiple sequence alignment

## Description

showalign displays an aligned set of protein or a nucleic acid sequences in a style suitable for publication.

The output is sent to the screen by default for the user to view, but it can write the results to a file.

The output highlights various differences or similarities between each of the sequences and a reference sequence by setting selected types of matches to a reference sequence to be '.' characters.

The reference sequence can be either the calculated consensus sequence (the default) or it can be one of the set of aligned sequences, specified by either the ordinal number of that sequence in the input file, or by its name.

The output sequences can be displayed in either the input order (the default) or they can be sorted in order of their similarity to the reference sequence or sorted alphabetically by their names.

By using the '-show' option, the displayed sequences can either be shown as:

- complete (-show=All),
- only identical matches between the sequence and the reference sequence, all other positions being replaced by '.' characters (-show=Identities)
- non-identical matches, with identical matches being replaced by '.' characters, similar matches are shown in lower case (-show=Non-identities)
- similar matches, with non-similar matches being replaced by '.' characters, similar matches are shown in lower case (-show=Similarities)
- dissimilar matches, with identical or similar matches being replaced by '.' characters (-show=Dissimilarities)

A small table of the way these alignments are displayed illustrates this.
If we have a reference protein sequence of "III" and a sequence aligned to this of "ILW", then we have an identical matching residue, then a similar one, then a dissimilar one.
The different methods of display would give the following:

    Reference       III

    All             ILw
    Identical       I..
    Non-id          .lW
    Similar         Il.
    Dissimilar      ..W

Changing the similar matches to lowercase can optionally be disable by using the option -nosimilarcase.

The displayed sequence can be numbered by placing a ruler with ticks above the sequence.

The width of a line can be set. The width of a margin to the left of the sequences that shows the sequence names can be set.

Specified regions of the sequence can be displayed in uppercase to highlight them.

The output can be formatted for HTML.

If the output is being formatted for HTML, then specified regions of the sequence can be displayed in any valid HTML colours.

### The consensus line

The consensus line can be displayed in a mixture of uppercase and lowercase symbols.

The uppercase consensus symbol is meant to indicate that the consensus is strong and lowercase indicates that it is weak. In practice, I don't really like this feature and genarally turn it off.

The cutoff for setting the case of the consensus is set by the qualifier '-setcase'. If the score of the matches is above this value, then the symbol is in uppercase, iot the score is below the -setcase value then the symbol is in lowercase.

To put all of the consensus symbols into uppercase or lowercase, make -setcase very low (try -100000 ?) or very large (try 100000 ?).

## Usage

Here is a sample session with showalign:

    % showalign
    Display a multiple sequence alignment
    Input sequence set: globin.seq
    Output file [stdout]:
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpkv
    HBB_MACFU ....P...n...T.....................................P....G....
    HBD_HUMAN ....P...t..NA........A............................P....G....
    HBB_RABIT ...sS.......A.......e.............................An...N....
    HBB_BOVIN -M..A...a...AF....K..........-...................tA....N....
    HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N....
    HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG....
    HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G....
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpkv

                      70        80        90       100       110       120
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus kahgkkvlxsfxdglXhldnlkgtfaklselhcdxxhvdpenfkllgnvlvivlaxhfgk
    HBB_MACFU ........Ga.S...N..........q.......--...............C...H....
    HBD_HUMAN ........Ga.S...A.........sq.......--.......r.......C...Rn...
    HBB_RABIT ........Aa.Se..S..................KL.......r..........sH....
    HBB_BOVIN ........D..Sn.mK...d......A.......KL...............v...Rn...
    HBB_LAMGL ....S...N..G...S........y.........KL.......r.......v...R....
    HBE_HUMAN ........T..G.AiKnm....PA..........--.............m..i..T....
    HBE_RABIT ........T..G.AiKnm.....A..........--..............l....T....
    Consensus kahgkkvlxsfxdglXhldnlkgtfaklselhcdxxhvdpenfkllgnvlvivlaxhfgk

                     130       140       150       160       170       180
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus eftpqvqaayqkvvagvanalahkyhxxxx
    HBB_MACFU ..........................
    HBD_HUMAN .....m....................
    HBB_RABIT ..........................
    HBB_BOVIN ....Vl..Df.............r..
    HBB_LAMGL ....Dl.................r..ACDH
    HBE_HUMAN ....e....w..l.sA
    HBE_RABIT ....e....w..l.s...I.......
    Consensus eftpqvqaayqkvvagvanalahkyhxxxx

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqset     The sequence alignment to be displayed.
      [-outfile]           outfile    If you enter the name of a file here then
                                      this program will write the sequence details
                                      into that file.

       Optional qualifiers:
       -refseq             string     If you give the number in the alignment or
                                      the name of a sequence, it will be taken to
                                      be the reference sequence. The reference
                                      sequence is always show in full and is the
                                      one against which all the other sequences
                                      are compared. If this is set to 0 then the
                                      consensus sequence will be used as the
                                      reference sequence. By default the consensus
                                      sequence is used as the reference sequence.
       -[no]bottom         bool       If this is true then the refernce sequence
                                      is displayed at the bottom of the alignment
                                      as well as at the top.
       -show               menu       What to show
       -order              menu       Output order of the sequences
       -[no]similarcase    bool       If this is set True, then when -show is set
                                      to 'Similarities' or 'Non-identities' and a
                                      residue is similar but not identical to the
                                      reference sequence residue, it will be
                                      changed to lower-case. If -show is set to
                                      'All' then non-identical, non-similar
                                      residues will be changed to lower-case. If
                                      this is False then no change to the case of
                                      the residues is made on the basis of their
                                      similarity to the reference sequence.
       -matrix             matrix     Similarity scoring Matrix file
       -[no]consensus      bool       If this is true then the consensus line is
                                      displayed at the bottom.

       Advanced qualifiers:
       -uppercase          range      Regions to put in uppercase.
                                      If this is left blank, then the sequence
                                      case is left alone.
                                      A set of regions is specified by a set of
                                      pairs of positions.
                                      The positions are integers.
                                      They are separated by any non-digit,
                                      non-alpha character.
                                      Examples of region specifications are:
                                      24-45, 56-78
                                      1:45, 67=99;765..888
                                      1,5,8,10,23,45,57,99
       -[no]number         bool       If this option is true then a line giving
                                      the positions in the alignment is displayed
                                      every 10 characters above the alignment.
       -[no]ruler          bool       If this option is true then a ruler line
                                      marking every 5th and 10th character in the
                                      alignment is displayed.
       -width              integer    Width of sequence to display
       -margin             integer    This sets the length of the left-hand margin
                                      for sequence names. If the margin is set at
                                      0 then no margin and no names are
                                      displayed. If the margin is set to a value
                                      that is less than the length of a sequence
                                      name then the sequence name is displayed
                                      truncated to the length of the margin. If
                                      the margin is set to -1 then the minimum
                                      margin width that will allow all the
                                      sequence names to be displayed in full plus
                                      a space at the end of the name will
                                      automatically be selected.
       -[no]names          bool       Set this to be false if you do not wish to
                                      display the ID name of the sequences
       -html               bool       Use HTML formatting
       -highlight          range      Regions to colour if formatting for HTML.
                                      If this is left blank, then the sequence is
                                      left alone.
                                      A set of regions is specified by a set of
                                      pairs of positions.
                                      The positions are integers.
                                      They are followed by any valid HTML font
                                      colour.
                                      Examples of region specifications are:
                                      24-45 blue 56-78 orange
                                      1-100 green 120-156 red
                                      A file of ranges to colour (one range per
                                      line) can be specified as '@filename'.
       -plurality          float      Set a cut-off for the % of positive scoring
                                      matches below which there is no consensus.
                                      The default plurality is taken as 50% of the
                                      total weight of all the sequences in the
                                      alignment.
       -setcase            float      Sets the threshold for the scores of the
                                      positive matches above which the consensus
                                      is is upper-case and below which the
                                      consensus is in lower-case.
       -identity           float      Provides the facility of setting the
                                      required number of identities at a position
                                      for it to give a consensus. Therefore, if
                                      this is set to 100% only columns of
                                      identities contribute to the consensus.

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | The sequence alignment to be displayed. | Readable sequences | Required
[-outfile] (Parameter 2) | If you enter the name of a file here then this program will write the sequence details into that file. | Output file | stdout
Optional qualifiers | Allowed values | Default
-refseq | If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is always show in full and is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence. | Any string is accepted | 0
-[no]bottom | If this is true then the refernce sequence is displayed at the bottom of the alignment as well as at the top. | Yes/No | Yes
-show | What to show |
A | (All of the sequences)
I | (Identities between the sequences)
N | (Non-identities between the sequences)
S | (Similarities between the sequences)
D | (Dissimilarities between the sequences)
| N
-order | Output order of the sequences |
I | (Input order - no change)
A | (Alphabetical order of the names)
S | (Similarity to the reference sequence)
| I
-[no]similarcase | If this is set True, then when -show is set to 'Similarities' or 'Non-identities' and a residue is similar but not identical to the reference sequence residue, it will be changed to lower-case. If -show is set to 'All' then non-identical, non-similar residues will be changed to lower-case. If this is False then no change to the case of the residues is made on the basis of their similarity to the reference sequence. | Yes/No | Yes
-matrix | Similarity scoring Matrix file | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA
-[no]consensus | If this is true then the consensus line is displayed at the bottom. | Yes/No | Yes
Advanced qualifiers | Allowed values | Default
-uppercase | Regions to put in uppercase. If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 | Sequence range | If this is left blank, then the sequence case is left alone.
-[no]number | If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment. | Yes/No | Yes
-[no]ruler | If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed. | Yes/No | Yes
-width | Width of sequence to display | Integer 1 or more | 60
-margin | This sets the length of the left-hand margin for sequence names. If the margin is set at 0 then no margin and no names are displayed. If the margin is set to a value that is less than the length of a sequence name then the sequence name is displayed truncated to the length of the margin. If the margin is set to -1 then the minimum margin width that will allow all the sequence names to be displayed in full plus a space at the end of the name will automatically be selected. | Integer -1 or more | -1
-[no]names | Set this to be false if you do not wish to display the ID name of the sequences | Yes/No | Yes
-html | Use HTML formatting | Yes/No | No
-highlight | Regions to colour if formatting for HTML. If this is left blank, then the sequence is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are followed by any valid HTML font colour. Examples of region specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A file of ranges to colour (one range per line) can be specified as '@filename'. | Sequence range | full sequence
-plurality | Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment. | Number from 0.000 to 100.000 | 50.0
-setcase | Sets the threshold for the scores of the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case. | Any integer value | 0
-identity | Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus. | Number from 0.000 to 100.000 | 0.0

## Input file format

showalign reads in a set of aligned protein or nucleic sequences.

You can specifiy a file of ranges to display in uppercase by giving the '-uppercase' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-upper @myfile').

The format of the range file is:

- Comment lines start with '#' in the first column.
- Comment lines and blank lines are ignored.
- The line may start with white-space.
- There are two positive (integer) numbers per line separated by one or more space or
- TAB characters.
- The second number must be greater or equal to the first number.
- There can be optional text after the two numbers to annotate the line.
- White-space before or after the text is removed.

An example range file is:

    # this is my set of ranges
    12   23
     4   5       this is like 12-23, but smaller
    67   10348   interesting region

You can specifiy a file of ranges to highlight in a different colour when outputting in HTML format (using the '-html' qualifier) by giving the '-highlight' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-highlight @myfile').

The format of this file is very similar to the format of the above uppercase range file, except that the text after the start and end positions is used as the HTML colour name. This colour name is used 'as is' when specifying the colour in HTML in a '' construct, (where 'xxx' is the name of the colour).

The standard names of HTML font colours are given in:
http://http://www.w3.org/TR/REC-html40/types.html and http://www.ausmall.com.au/freegraf/ncolour2.htm and http://mindprod.com/htmlcolours.html (amongst other places).

An example highlight range file is:

    # this is my set of ranges
    12   23         red
     4   5          darkturquoise
    67   10348      #FFE4E1

## Output file format

showalign writes out a text file, optionally formatted for HTML.

Some examples of different optional output styles follows:

    % showalign g.seq stdout -show=n
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
    HBB_MACFU ....P...n...T.....................................P....G...
    HBD_HUMAN ....P...t..NA........A............................P....G...
    HBB_RABIT ...sS.......A.......e.............................An...N...
    HBB_BOVIN -M..A...a...AF....K..........-...................tA....N...
    HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N...
    HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG...
    HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G...
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    % showalign g.seq stdout -show=a
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
    HBB_MACFU VHLTpEEKNAVTtLWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSSpDAVMgNPK
    HBD_HUMAN VHLTpEEKTAVnaLWGKVNVDaVGGEALGRLLVVYPWTQRFFESFGDLSSpDAVMgNPK
    HBB_RABIT VHLSsEEKSAVTaLWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSSaNAVMnNPK
    HBB_BOVIN -mLTaEEKAAVTafWGKVkVDEVGGEALG-LLVVYPWTQRFFESFGDLSTaDAVMnNPK
    HBB_LAMGL VNLSgDEKNAVhgLWsKVkVDEVGGEALG-LLVVYPWTRRFFESFGDLSTaDAVMnNPK
    HBE_HUMAN VHfTaEEKAAVTsLWsKMNVEEaGGEALGRLLVVYPWTQRFFDSFGNLSSpsAILgNPK
    HBE_RABIT VHfTpEEKciISkqWGQVNIDEtGGEALGRLLVVYPWTQRFFDNFGNLSSssAIMgNPK
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    % showalign g.seq stdout -show=i
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
    HBB_MACFU VHLT.EEK.AVT.LWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSS.DAVM.NPK
    HBD_HUMAN VHLT.EEK.AV..LWGKVNVD.VGGEALGRLLVVYPWTQRFFESFGDLSS.DAVM.NPK
    HBB_RABIT VHL..EEKSAVT.LWGKVNV.EVGGEALGRLLVVYPWTQRFFESFGDLSS..AVM.NPK
    HBB_BOVIN -.LT.EEK.AVT..WGKV.VDEVGGEALG-LLVVYPWTQRFFESFGDLS..DAVM.NPK
    HBB_LAMGL V.L...EK.AV..LW.KV.VDEVGGEALG-LLVVYPWT.RFFESFGDLS..DAVM.NPK
    HBE_HUMAN VH.T.EEK.AVT.LW.K.NV.E.GGEALGRLLVVYPWTQRFF.SFG.LSS..A...NPK
    HBE_RABIT VH.T.EEK......WG.VN.DE.GGEALGRLLVVYPWTQRFF..FG.LSS..A.M.NPK
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    % showalign g.seq stdout -show=s
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
    HBB_MACFU VHLT.EEKnAVT.LWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSS.DAVM.NPK
    HBD_HUMAN VHLT.EEKtAV..LWGKVNVD.VGGEALGRLLVVYPWTQRFFESFGDLSS.DAVM.NPK
    HBB_RABIT VHLs.EEKSAVT.LWGKVNVeEVGGEALGRLLVVYPWTQRFFESFGDLSS.nAVM.NPK
    HBB_BOVIN -.LT.EEKaAVT..WGKV.VDEVGGEALG-LLVVYPWTQRFFESFGDLSt.DAVM.NPK
    HBB_LAMGL VnLs.dEKnAV..LW.KV.VDEVGGEALG-LLVVYPWTrRFFESFGDLSt.DAVM.NPK
    HBE_HUMAN VH.T.EEKaAVT.LW.KmNVeE.GGEALGRLLVVYPWTQRFFdSFGnLSS..Ail.NPK
    HBE_RABIT VH.T.EEK..is..WGqVNiDE.GGEALGRLLVVYPWTQRFFdnFGnLSS..AiM.NPK
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    % showalign g.seq stdout -show=d
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
    HBB_MACFU ....P.......T.....................................P....G...
    HBD_HUMAN ....P......NA........A............................P....G...
    HBB_RABIT ....S.......A.....................................A....N...
    HBB_BOVIN -M..A.......AF....K..........-....................A....N...
    HBB_LAMGL ....G......HG..S..K..........-....................A....N...
    HBE_HUMAN ..F.A.......S..S......A...........................PS...G...
    HBE_RABIT ..F.P...CI..KQ........T...........................SS...G...
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    % showalign g.seq stdout -ref=1
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    HBB_MACFU VHLTPEEKNAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPK
    HBD_HUMAN ........T..NA........A.....................................
    HBB_RABIT ...sS...s...A.......e.............................An...N...
    HBB_BOVIN -M..A...A...AF....K..........-...................tA....N...
    HBB_LAMGL .n.sGd.....HG..S..K..........-........r..........tA....N...
    HBE_HUMAN ..F.A...A...s..S.m..e.A...................d...n....S.il....
    HBE_RABIT ..F.....CIisKQ..q..i..T...................dn..n...SS.i.....
    HBB_MACFU VHLTPEEKNAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPK
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    Display a range of sequences in uppercase, everything else in lowercase
    % showalign g.seq stdout -nocon -ref=1 -sl -upper 9-15 -nosimilarcaseDisplay a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    HBB_MACFU vhltpeekNAVTTLWgkvnvdevggealgrllvvypwtqrffesfgdlsspdavmgnpk
    HBD_HUMAN ........T..NA........a.....................................
    HBB_RABIT ...ss...S...A.......e.............................an...n...
    HBB_BOVIN -m..a...A...AF....k..........-...................ta....n...
    HBB_LAMGL .n.sgd.....HG..s..k..........-........r..........ta....n...
    HBE_HUMAN ..f.a...A...S..s.m..e.a...................d...n....s.il....
    HBE_RABIT ..f.....CIISKQ..q..i..t...................dn..n...ss.i.....
    HBB_MACFU vhltpeekNAVTTLWgkvnvdevggealgrllvvypwtqrffesfgdlsspdavmgnpk

    Alphabetical order
    % showalign g.seq stdout -order=a
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
    HBB_BOVIN -M..A...a...AF....K..........-...................tA....N...
    HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N...
    HBB_MACFU ....P...n...T.....................................P....G...
    HBB_RABIT ...sS.......A.......e.............................An...N...
    HBD_HUMAN ....P...t..NA........A............................P....G...
    HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG...
    HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G...
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    In order of similarity to the reference sequence
    % showalign g.seq stdout -order=s
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
    HBB_MACFU ....P...n...T.....................................P....G...
    HBB_RABIT ...sS.......A.......e.............................An...N...
    HBD_HUMAN ....P...t..NA........A............................P....G...
    HBB_BOVIN -M..A...a...AF....K..........-...................tA....N...
    HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG...
    HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N...
    HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G...
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    Format for HTML and highlight some inetersting regions in different colours
    % showalign g.seq stdout -html -high '4-13 green 43-43 red 51-56 blue'
    Display a multiple sequence alignment
                      10        20        30        40        50        60
              ----:----|----:----|----:----|----:----|----:----|----:----|
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
    HBB_MACFU ....P...n...T.....................................P....G...
    HBD_HUMAN ....P...t..NA........A............................P....G...
    HBB_RABIT ...sS.......A.......e.............................An...N...
    HBB_BOVIN -M..A...a...AF....K..........-...................tA....N...
    HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N...
    HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG...
    HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G...
    Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk

    No consensus line at the bottom
    No ruler line
    No numbers line
    Don't repeat the reference sequence at the bottom of the sequences
    Use sequence 1 as the reference sequence
    Display residues from position 10 to 30 only
    % showalign g.seq stdout -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30
    Display a multiple sequence alignment

    HBB_MACFU AVTTLWGKVNVDEVGGEALGR
    HBD_HUMAN ..NA........A........
    HBB_RABIT ...A.......e.........
    HBB_BOVIN ...AF....K..........-
    HBB_LAMGL ..HG..S..K..........-
    HBE_HUMAN ...s..S.m..e.A.......
    HBE_RABIT IisKQ..q..i..T.......

## Data files

showalign reads in scoring matrices to determine the consesnus sequence and to determine which matches are similar or not.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
abiview | Reads ABI file and display the trace
cirdna | Draws circular maps of DNA constructs
emma | Multiple alignment program - interface to ClustalW program
infoalign | Information on a multiple sequence alignment
lindna | Draws linear maps of DNA constructs
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
plotcon | Plots the quality of conservation of a sequence alignment
prettyplot | Displays aligned sequences, with colouring and boxing
prettyseq | Output sequence with translated ranges
remap | Display a sequence with restriction cut sites, translation etc
seealso | Finds programs sharing group names
showdb | Displays information on the currently available databases
showfeat | Show features of a sequence
showseq | Display a sequence with features, translation etc
textsearch | Search sequence documentation text. SRS and Entrez are faster!
tranalign | Align nucleic coding regions given the aligned proteins

## Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## History

Written (23 May 2001) - Gary Williams

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments