                                  showalign



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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Display a multiple sequence alignment in pretty format

Description

   showalign reads a set of aligned protein or a nucleic acid sequences,
   and writes them to file (or screen) in a style suitable for
   publication. Similarities and differences of each sequence to a
   reference sequence are highlighted for specified types of matches. The
   reference sequence can be the calculated consensus sequence (default)
   or one of the input set (specified by name or the ordinal number of
   that sequence in the file). The output sequences can be displayed in
   either the input order (the default), sorted in order of their
   similarity to the reference sequence, or sorted alphabetically by their
   names. There are many other options to control the content and format
   of the output.

Usage

   Here is a sample session with showalign


% showalign
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the input files for this example
   Go to the output files for this example

   Example 2

   Display the sequences in order of similarity to the reference sequence


% showalign -order=s
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 3

   Format for HTML and highlight some interesting regions in different
   colours:


% showalign -html -high "4-13 green 43-43 red 51-56 blue"
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 4

   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 -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 5

   Show non-identities between the sequences


% showalign -show=n
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Example 6

   Show all of the sequences


% showalign -show=a
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 7

   Show identities between the sequences


% showalign -show=i
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 8

   Show similarities between the sequences


% showalign -show=s
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 9

   Show dissimilarities between the sequences


% showalign -show=d
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 10

   Use the first sequence as the reference to compare to:


% showalign -ref=1
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 11

   Show a range of sequences in uppercase, everything else in lowercase


% showalign -nocon -ref=1 -sl -upper 9-15 -nosimilarcase
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

   Example 12

   Display the sequences in alphabetic order:


% showalign -order=a
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:


   Go to the output files for this example

Command line arguments

Display a multiple sequence alignment in pretty format
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     The sequence alignment to be displayed.
  [-outfile]           outfile    [*.showalign] Output file name

   Additional (Optional) qualifiers:
   -matrix             matrix     [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.
   -refseq             string     [0] 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 shown 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)
   -[no]bottom         boolean    [Y] If this is true then the reference
                                  sequence is displayed at the bottom of the
                                  alignment instead of the top.
   -show               menu       [N] What to show (Values: 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))
   -order              menu       [I] Output order of the sequences (Values: I
                                  (Input order - no change); A (Alphabetical
                                  order of the names); S (Similarity to the
                                  reference sequence))
   -[no]similarcase    boolean    [Y] 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.
   -[no]consensus      boolean    [Y] If this is true then the consensus line
                                  is displayed.

   Advanced (Unprompted) qualifiers:
   -uppercase          range      [If this is left blank, then the sequence
                                  case is left alone.] 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         boolean    [Y] If this option is true then a line
                                  giving the positions in the alignment is
                                  displayed every 10 characters above the
                                  alignment.
   -[no]ruler          boolean    [Y] If this option is true then a ruler line
                                  marking every 5th and 10th character in the
                                  alignment is displayed.
   -width              integer    [60] Width of sequence to display (Integer 1
                                  or more)
   -margin             integer    [-1] 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)
   -html               boolean    [N] Use HTML formatting
   -highlight          range      [(full sequence)] 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      [50.0] 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)
   -setcase            float      [@( $(sequence.totweight) / 2)] Sets the
                                  threshold for the scores of the positive
                                  matches above which the consensus is in
                                  upper-case and below which the consensus is
                                  in lower-case. By default this is set to be
                                  half of the (weight-adjusted) number of
                                  sequences in the alignment. (Any numeric
                                  value)
   -identity           float      [0.0] 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)
   -[no]gaps           boolean    [Y] If this option is true then gap
                                  characters can appear in the consensus. The
                                  alternative is 'N' for nucleotide, or 'X'
                                  for protein

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

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

  Input files for usage example

  File: globins.msf

!!AA_MULTIPLE_ALIGNMENT 1.0

  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.61
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43

//

           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~


   You can specify 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 specify 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#h-6.5

   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.

  Output files for usage example

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------VH.tPE.K.A.TaL.G.V.-VD....E..GR-.LVvY.WT.R..Es.GD..T
HBB_HORSE  --------VQ..GE.KaA.LaL.D.V.-EE....E..GR-.LVvY.WT.R..Ds.GD..N
HBA_HUMAN  --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PT.KTYFPH
HBA_HORSE  --------------VL.AADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PT.KTYFPH
MYG_PHYCA  -------VLSEGEWqLVLHVWAKVeAd-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KT
GLB5_PETMA PIVDTGSVAP..AA.KtKiR.A.APVYSTY.TS.VDiLVKFFTST.AA.E..PK.KG.tT
LGB2_LUPLU --------GA.tESqAaL.K.S.EeF.ANIPKHTHRFFILvLE.A.AAkDL.SFLKGT.E
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..Gn
HBB_HORSE  PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..Gn
HBA_HUMAN  F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.
HBA_HORSE  F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.
MYG_PHYCA  EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSE
GLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKV
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKE
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

                  130       140       150       160
           ----:----|----:----|----:----|----:----|----
HBB_HUMAN  V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------
HBB_HORSE  V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------
HBA_HUMAN  C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------
HBA_HORSE  C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------
MYG_PHYCA  AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQG
GLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------
LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx


  Output files for usage example 2

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------VH.tPE.K.A.TaL.G.V.-VD....E..GR-.LVvY.WT.R..Es.GD..T
HBB_HORSE  --------VQ..GE.KaA.LaL.D.V.-EE....E..GR-.LVvY.WT.R..Ds.GD..N
HBA_HORSE  --------------VL.AADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PT.KTYFPH
HBA_HUMAN  --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PT.KTYFPH
GLB5_PETMA PIVDTGSVAP..AA.KtKiR.A.APVYSTY.TS.VDiLVKFFTST.AA.E..PK.KG.tT
MYG_PHYCA  -------VLSEGEWqLVLHVWAKVeAd-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KT
LGB2_LUPLU --------GA.tESqAaL.K.S.EeF.ANIPKHTHRFFILvLE.A.AAkDL.SFLKGT.E
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..Gn
HBB_HORSE  PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..Gn
HBA_HORSE  F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.
HBA_HUMAN  F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.
GLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKV
MYG_PHYCA  EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSE
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKE
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

                  130       140       150       160
           ----:----|----:----|----:----|----:----|----
HBB_HUMAN  V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------
HBB_HORSE  V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------
HBA_HORSE  C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------
HBA_HUMAN  C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------
GLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------
MYG_PHYCA  AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQG
LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx

  Output files for usage example 3

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------VH.tPE.K.A.TaL.G.V.-VD....E..GR-.L<f
ont color=red>VvY.WT.R..Es.GD..T
HBB_HORSE  --------VQ..GE.KaA.LaL.D.V.-EE....E..GR-.L<f
ont color=red>VvY.WT.R..Ds.GD..N
HBA_HUMAN  --------------VL.PADKTNV.AA-WGk..AH.GEYGAE<f
ont color=red>AlERMFLS.PT.KTYFPH
HBA_HORSE  --------------VL.AADKTNV.AA-WSk...H.GEYGAE<f
ont color=red>AlERMFLG.PT.KTYFPH
MYG_PHYCA  -------VLSEGEWqLVLHVWAKVeAd-VAGH.QDI.IR-.F<f
ont color=red>KSH.ETLEK.DR.KH.KT
GLB5_PETMA PIVDTGSVAP..AA.KtKiR.A.APVYSTY.TS.VDiLVKFF<f
ont color=red>TST.AA.E..PK.KG.tT
LGB2_LUPLU --------GA.tESqAaL.K.S.EeF.ANIPKHTHRFFILvL<f
ont color=red>E.A.AAkDL.SFLKGT.E
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLx<f
ont color=red>xIxPxxQxFFxTFxxLSx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..Gn
HBB_HORSE  PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..Gn
HBA_HUMAN  F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.
HBA_HORSE  F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.
MYG_PHYCA  EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSE
GLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKV
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKE
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

                  130       140       150       160
           ----:----|----:----|----:----|----:----|----
HBB_HUMAN  V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------
HBB_HORSE  V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------
HBA_HUMAN  C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------
HBA_HORSE  C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------
MYG_PHYCA  AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQG
GLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------
LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx

  Output files for usage example 4

  File: globins.showalign

HBB_HUMAN  HLTPEEKSAVTALWGKVN-VD
HBB_HORSE  Q.sG...a..L...D...-Ee
HBA_HUMAN  -----VL.PADKTNV.AA-WG
HBA_HORSE  -----VL..ADKTNV.AA-WS
MYG_PHYCA  SEGEWqLVLHVWAKVeAd-.A
GLB5_PETMA P.sAA..tKiRsA.AP.YSTY
LGB2_LUPLU A..ESqAaL.KsS.EeF.ANI

  Output files for usage example 6

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------vhLTpeEkSaVtAlWgKvN-vdEVGGeALgr-LlvVyPwtQrFFeSFgdLSt
HBB_HORSE  --------vqLSgeEkAaVlAlWdKvN-eeEVGGeALgr-LlvVyPwtQrFFdSFgdLSn
HBA_HUMAN  --------------vlSpadktnvKaa-wgKVGahAgeygaeaLermflsFptTktyfph
HBA_HORSE  --------------vlSaadktnvKaa-wsKVGGhAgeygaeaLermflgFptTktyfph
MYG_PHYCA  -------vlsegewQlvlhvwakvEaD-vaghGqdiLir-LfkshPetlekFdrFkhLkt
GLB5_PETMA pivdtgsvapLSaaEkTkIrSaWapvystyEtsGvdIlvkfftstPaaQeFFpkFkgLTt
LGB2_LUPLU --------gaLTesQaAlVkSsWeEfNanipkhthrffilVleIaPaaKdlFsflkgtSe
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  pDaVmGNpKVKaHGKKVLgAfsDgLaHLDNLKgtfAtLSELHcdKLh--VDPeNFRLLgN
HBB_HORSE  pgaVmGNpKVKaHGKKVLhSfgEgVhHLDNLKgtfAaLSELHcdKLh--VDPeNFRLLgN
HBA_HUMAN  fDlshGSaQVKgHGKKVadALtNaVaHVDDMpnalSaLSDLHAhKLR--VDPvNFKLLsH
HBA_HORSE  fDlshGSaQVKaHGKKVgdALtlaVgHLDDLpgalSnLSDLHAhKLR--VDPvNFKLLsH
MYG_PHYCA  eaeMkaSedLKkHGvtVLtALgaiLkkkghhEaelkpLAqsHAtKhK--IpikylEfIse
GLB5_PETMA aDqLkkSadVRwHaERIInAVnDaVasMDDtEkmsmkLrDLsgkhaK--sfqvDpQyfkv
LGB2_LUPLU vpqnnpelQahagkvfkLvyeaaiqlqVtgVvvtdAtLkNLgSvhVskgVadaHFpVVke
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

                  130       140       150       160
           ----:----|----:----|----:----|----:----|----
HBB_HUMAN  vLVcVLAhHfgkEFTPpVqAAyqKvVAgVAnaLahKYh------
HBB_HORSE  vLVvVLArHfgkDFTPELqASyqKvVAgVAnaLahKYh------
HBA_HUMAN  cLLvtLAaHlpaEFTPaVhASLdKfLAsVStvLtsKYr------
HBA_HORSE  cLLstLAvHlpnDFTPaVhASLdKfLSsVStvLtsKYr------
MYG_PHYCA  aIIhVLhsrhpgDFgaDaqgAMnKaLelfrkdIaaKYkelgyqg
GLB5_PETMA laavIadtvaagDagfEklmSMiciLlrsAy-------------
LGB2_LUPLU aILktIkevvgakWSeELnSAwtiaydeLAivIkkEmndaa---
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx


  Output files for usage example 7

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------..L...E.S.V...W.K.N-..EVGG.AL..-L....P..Q.FF..F..LS.
HBB_HORSE  --------..LS..E...V...W.K.N-..EVGG.AL..-L....P..Q.FF..F..LS.
HBA_HUMAN  --------------..S.......K..-...VG..A..............F..T......
HBA_HORSE  --------------..S.......K..-...VGG.A..............F..T......
MYG_PHYCA  -------....................-....G...L..-L....P.....F..F..L..
GLB5_PETMA ..........LS..E.....S.W.......E..G...........P..Q.FF..F..L..
LGB2_LUPLU --------..L.......V.S.W...N................I.P.....F......S.
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  .D...G...VK.HGKKVL.A..D...HLD.L....A.LS.LH..KL.--VDP.NF.LL..
HBB_HORSE  .....G...VK.HGKKVL......V.HLD.L....A.LS.LH..KL.--VDP.NF.LL..
HBA_HUMAN  .D...GS.QVK.HGKKV..AL...V.H.DD.......LSDLHA.KLR--VDP.NFKLL.H
HBA_HORSE  .D...GS.QVK.HGKKV..AL...V.HLDDL......LSDLHA.KLR--VDP.NFKLL.H
MYG_PHYCA  ...M..S...K.HG..VL.AL..........E.....L...HA.K..--...........
GLB5_PETMA .D....S..V..H......A..D.V...DD.E.....L.DL......--...........
LGB2_LUPLU ........Q........L.................A.L..L........V....F.....
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

                  130       140       150       160
           ----:----|----:----|----:----|----:----|----
HBB_HUMAN  .L..VLA.H....FTP.V.A...K..A.VA..L..KY.------
HBB_HORSE  .L..VLA.H...DFTPE..AS..K..A.VA..L..KY.------
HBA_HUMAN  .LL..LA.H....FTP.V.AS..K.LA.V...L..KY.------
HBA_HORSE  .LL..LA.H...DFTP.V.AS..K.L..V...L..KY.------
MYG_PHYCA  ....VL......DF.......M.K.L.........KY.......
GLB5_PETMA ............D...E...SM...L...A.-------------
LGB2_LUPLU ..L.............E............A...........---
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx


  Output files for usage example 8

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------..Lt..E.S.V.a.W.K.N-..EVGG.AL..-L..v.P..Q.FF.sF..LS.
HBB_HORSE  --------..LS..E.a.V.a.W.K.N-..EVGG.AL..-L..v.P..Q.FF.sF..LS.
HBA_HUMAN  --------------..S.......K..-..kVG..A.......l......F..T......
HBA_HORSE  --------------..S.......K..-..kVGG.A.......l......F..T......
MYG_PHYCA  -------.......q.........e.d-....G...L..-L....P.....F..F..L..
GLB5_PETMA ..........LS..E.t.i.S.W.......E..G..i........P..Q.FF..F..Lt.
LGB2_LUPLU --------..Lt..q.a.V.S.W.e.N.............v..I.P..k..F......S.
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  .D.v.Gn.kVK.HGKKVL.A..D.l.HLDnLk...A.LSeLH..KL.--VDP.NFrLL.n
HBB_HORSE  ...v.Gn.kVK.HGKKVL.s..e.V.HLDnLk...A.LSeLH..KL.--VDP.NFrLL.n
HBA_HUMAN  .D...GS.QVK.HGKKV..AL.n.V.HvDDm....s.LSDLHA.KLR--VDP.NFKLL.H
HBA_HORSE  .D...GS.QVK.HGKKV..AL...V.HLDDL....s.LSDLHA.KLR--VDP.NFKLL.H
MYG_PHYCA  ...M..S..lK.HG..VL.AL...l......E.....La..HA.K.k--i.....e.i..
GLB5_PETMA .D.l..S..Vr.H.erii.Av.D.V..mDD.E.....L.DL.....k--....d.q....
LGB2_LUPLU ........Q........L.........v..v....A.L.nL.s..v...V...hF.vv..
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

                  130       140       150       160
           ----:----|----:----|----:----|----:----|----
HBB_HUMAN  .Lv.VLA.H...eFTP.V.Aa..K.vA.VA..L..KY.------
HBB_HORSE  .Lv.VLA.H...DFTPEl.AS..K.vA.VA..L..KY.------
HBA_HUMAN  .LL..LA.H...eFTP.V.ASl.K.LA.Vs..L..KY.------
HBA_HORSE  .LL..LA.H...DFTP.V.ASl.K.Ls.Vs..L..KY.------
MYG_PHYCA  .ii.VL......DF..d...aM.K.L......i..KY.......
GLB5_PETMA ....i.......D...E...SM...L...A.-------------
LGB2_LUPLU .iL..i.......ws.El.sa.......lA..i..e.....---
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx


  Output files for usage example 9

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  --------VH..PE.K.A.T.L.G.V.-VD....E..GR-.LV.Y.WT.R..E..GD..T
HBB_HORSE  --------VQ..GE.K.A.L.L.D.V.-EE....E..GR-.LV.Y.WT.R..D..GD..N
HBA_HUMAN  --------------VL.PADKTNV.AA-WG...AH.GEYGAEA.ERMFLS.PT.KTYFPH
HBA_HORSE  --------------VL.AADKTNV.AA-WS....H.GEYGAEA.ERMFLG.PT.KTYFPH
MYG_PHYCA  -------VLSEGEW.LVLHVWAKV.A.-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KT
GLB5_PETMA PIVDTGSVAP..AA.K.K.R.A.APVYSTY.TS.VD.LVKFFTST.AA.E..PK.KG..T
LGB2_LUPLU --------GA..ES.A.L.K.S.E.F.ANIPKHTHRFFIL.LE.A.AA.DL.SFLKGT.E
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  P.A.M..P...A......G.FS.G.A......GTF.T.....CD..H--...E.....G.
HBB_HORSE  PGA.M..P...A......H.FG.G.H......GTF.A.....CD..H--...E.....G.
HBA_HUMAN  F.LSH..A...G.....AD..T.A.A.....PNAL.A......H...--...V.....S.
HBA_HORSE  F.LSH..A...A.....GD..TLA.G.....PGAL.N......H...--...V.....S.
MYG_PHYCA  EAE.KA.ED..K..VT..T..GAI.KKKGHH.AELKP..QS..T.H.--.PIKYL.F.SE
GLB5_PETMA A.Q.KK.AD..W.A....N..N.A.AS...T.KMSMK.R..SGKHA.--SFQV.P.YFKV
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQ.TG.VVTD.T.K..G.VH.SKG.ADA..P..KE
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

                  130       140       150       160
           ----:----|----:----|----:----|----:----|----
HBB_HUMAN  V..C...H.FGK....P.Q..YQ.V..G..NA.AH..H------
HBB_HORSE  V..V...R.FGK......Q..YQ.V..G..NA.AH..H------
HBA_HUMAN  C..VT..A.LPA....A.H...D.F..S..TV.TS..R------
HBA_HORSE  C..ST..V.LPN....A.H...D.F..S..TV.TS..R------
MYG_PHYCA  A..H..HSRHPG..GA.AQG..N.A.ELFRKD.AA..KELGYQG
GLB5_PETMA LAAV.ADTVAAG.AGF.KLM..ICI.LRS.Y-------------
LGB2_LUPLU A..KT.KEVVGAK..E..N..WTIAYDE..IV.KK.MNDAA---
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx


  Output files for usage example 10

  File: globins.showalign

                           10         20        30         40        50
           ...v....----:----|----:----.|----:----|.----:----|----:----|
HBB_HUMAN  --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQRFFESFGDLST
HBB_HORSE  --------.Q.sG...a..L...D...-Ee.........-............d......N
HBA_HUMAN  --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PTtKTYFPH
HBA_HORSE  --------------VL..ADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PTtKTYFPH
MYG_PHYCA  -------VlSEGEWqLVLHVWAKVeAd-.AGH.QdI.I.-.FKSh.E.LEK.dR.KH.K.
GLB5_PETMA PIVDTGSVAP.sAA..tKiRsA.AP.YSTY.TS.VDiLVKFFTST.AA.E..PK.KG.t.
LGB2_LUPLU --------GA..ESqAaL.KsS.EeF.ANIPKHTHRFFILv.EiA.AAkDL.SFLKGT.E
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx

                   60        70        80        90         100       110
           ----:----|----:----|----:----|----:----|----:--..--|----:---
HBB_HUMAN  PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH--VDPENFRLLGN
HBB_HORSE  .G................Hs.Ge.vH..........A..........--...........
HBA_HUMAN  F.LSH.sAq..G.....AD.LtnAv..v.dmPNALsA..d..AH..R--...V..k..Sh
HBA_HORSE  F.LSH.sAq........GD.LtLAvG...d.P.ALsN..d..AH..R--...V..k..Sh
MYG_PHYCA  EAEmKAsEDl.K..VT..T.LGAI.KKKGhHeAELKP.aqS.AT.HK--iPIkYLEFiSE
GLB5_PETMA A.QlKKsAD.rW.AeriiN.Vn.Av.Sm.dTeKMSMK.Rd.SGKHAK--SFQVdPqYFKV
LGB2_LUPLU VPQNNPELqAH.GKVFK.VYEaAIQLQvTGvVV.D...KN.GSVHvSKG.ADAh.PvvKE
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

           10       120       130       140
           -|----:----|----:----|----:----|----:-....v.
HBB_HUMAN  VLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
HBB_HORSE  ...V...R....d...El..s.................------
HBA_HUMAN  C.lVT..A.LPA....A.H.sLD.Fl.S.sTV.TS..R------
HBA_HORSE  C.lST..V.LPNd...A.H.sLD.FlsS.sTV.TS..R------
MYG_PHYCA  AiiH..HSRHPGd.GADA.G.MN.AlELFRKDi.A..KELGYQG
GLB5_PETMA lAAViADTVAAGdAGFEKLMsMICilLRS.Y-------------
LGB2_LUPLU AilKTiKEVV.AkwsEElNs.wTIAYDEl.IViKKeMnDAA---
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx


  Output files for usage example 11

  File: globins.showalign

                           10         20        30         40        50
           ...v....----:----|----:----.|----:----|.----:----|----:----|
HBB_HUMAN  --------VHLTPEEksavtalwgkvn-vdevggealgr-llvvypwtqrffesfgdlst
HBB_HORSE  --------.Q.SG...a..l...d...-ee.........-............d......n
HBA_HUMAN  --------------Vl.padktnv.aa-wgk..ah.geygaealermfls.pttktyfph
HBA_HORSE  --------------Vl..adktnv.aa-wsk...h.geygaealermflg.pttktyfph
MYG_PHYCA  -------vLSEGEWQlvlhvwakvead-.agh.qdi.i.-.fksh.e.lek.dr.kh.k.
GLB5_PETMA pivdtgsvAP.SAA..tkirsa.ap.ysty.ts.vdilvkfftst.aa.e..pk.kg.t.
LGB2_LUPLU --------GA..ESQaal.kss.eef.anipkhthrffilv.eia.aakdl.sflkgt.e

                   60        70        80        90         100       110
           ----:----|----:----|----:----|----:----|----:--..--|----:---
HBB_HUMAN  pdavmgnpkvkahgkkvlgafsdglahldnlkgtfatlselhcdklh--vdpenfrllgn
HBB_HORSE  .g................hs.ge.vh..........a..........--...........
HBA_HUMAN  f.lsh.saq..g.....ad.ltnav..v.dmpnalsa..d..ah..r--...v..k..sh
HBA_HORSE  f.lsh.saq........gd.ltlavg...d.p.alsn..d..ah..r--...v..k..sh
MYG_PHYCA  eaemkasedl.k..vt..t.lgai.kkkghheaelkp.aqs.at.hk--ipikylefise
GLB5_PETMA a.qlkksad.rw.aeriin.vn.av.sm.dtekmsmk.rd.sgkhak--sfqvdpqyfkv
LGB2_LUPLU vpqnnpelqah.gkvfk.vyeaaiqlqvtgvvv.d...kn.gsvhvskg.adah.pvvke

           10       120       130       140
           -|----:----|----:----|----:----|----:-....v.
HBB_HUMAN  vlvcvlahhfgkeftppvqaayqkvvagvanalahkyh------
HBB_HORSE  ...v...r....d...el..s.................------
HBA_HUMAN  c.lvt..a.lpa....a.h.sld.fl.s.stv.ts..r------
HBA_HORSE  c.lst..v.lpnd...a.h.sld.flss.stv.ts..r------
MYG_PHYCA  aiih..hsrhpgd.gada.g.mn.alelfrkdi.a..kelgyqg
GLB5_PETMA laaviadtvaagdagfeklmsmicillrs.y-------------
LGB2_LUPLU ailktikevv.akwseelns.wtiaydel.ivikkemndaa---


  Output files for usage example 12

  File: globins.showalign

                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
GLB5_PETMA PIVDTGSVAP..AA.KtKiR.A.APVYSTY.TS.VDiLVKFFTST.AA.E..PK.KG.tT
HBA_HORSE  --------------VL.AADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PT.KTYFPH
HBA_HUMAN  --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PT.KTYFPH
HBB_HORSE  --------VQ..GE.KaA.LaL.D.V.-EE....E..GR-.LVvY.WT.R..Ds.GD..N
HBB_HUMAN  --------VH.tPE.K.A.TaL.G.V.-VD....E..GR-.LVvY.WT.R..Es.GD..T
LGB2_LUPLU --------GA.tESqAaL.K.S.EeF.ANIPKHTHRFFILvLE.A.AAkDL.SFLKGT.E
MYG_PHYCA  -------VLSEGEWqLVLHVWAKVeAd-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KT
Consensus  xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx

                   70        80        90       100       110       120
           ----:----|----:----|----:----|----:----|----:----|----:----|
GLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKV
HBA_HORSE  F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.
HBA_HUMAN  F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.
HBB_HORSE  PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..Gn
HBB_HUMAN  P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..Gn
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKE
MYG_PHYCA  EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSE
Consensus  xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH

                  130       140       150       160
           ----:----|----:----|----:----|----:----|----
GLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------
HBA_HORSE  C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------
HBA_HUMAN  C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------
HBB_HORSE  V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------
HBB_HUMAN  V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------
LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---
MYG_PHYCA  AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQG
Consensus  xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx


Data files

   showalign reads in scoring matrices to determine the consensus 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

   showalign reads in a scoring matrix to determine the consensus sequence
   and to determine which matches are similar or not.

   By using the -show option, the displayed sequences can 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)

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

   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

   The consensus line can be displayed in a mixture of uppercase and
   lowercase symbols. Uppercase indicates a strong consensus and lowercase
   a weak one. The cutoff for setting the consensus case is set by the
   qualifier -setcase. If the number of residues at that position that
   match the consensus value is greater than this, then the symbol is in
   uppercase, otherwise the symbol is in lowercase. By default, the value
   of -setcase is set so that if there are more than 50% of residues
   identical to the consensus at that position, then the consensus is in
   uppercase. To put all of the consensus symbols into uppercase or
   lowercase, make -setcase zero or very large (try 100000 ?).

   Other display options include Sequence numbering 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.

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          Display the trace in an ABI sequencer file
   coderet          Extract CDS, mRNA and translations from feature tables
   edialign         Local multiple alignment of sequences
   emma             Multiple sequence alignment (ClustalW wrapper)
   entret           Retrieve sequence entries from flatfile databases and files
   extractalign     Extract regions from a sequence alignment
   infoalign        Display basic information about a multiple sequence alignment
   infoseq          Display basic information about sequences
   plotcon          Plot conservation of a sequence alignment
   prettyplot       Draw a sequence alignment with pretty formatting
   refseqget        Get reference sequence
   seqxref          Retrieve all database cross-references for a sequence entry
   seqxrefget       Retrieve all cross-referenced data for a sequence entry
   tranalign        Generate an alignment of nucleic coding regions from aligned
                    proteins
   variationget     Get sequence variations
   whichdb          Search all sequence databases for an entry and retrieve it

Author(s)

   Gary Williams formerly at:
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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

   None
