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<HTML>
<HEAD>
  <TITLE>
  EMBOSS: showalign
  </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">


<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
showalign
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Display a multiple sequence alignment in pretty format
<H2>
    Description
</H2>


<p><b>showalign</b> 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.</p>

<H2>
    Usage
</H2>
Here is a sample session with <b>showalign</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<p>
<b>Example 2</b>
<p>
Display the sequences in order of similarity to the reference sequence 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>
<p>
<b>Example 3</b>
<p>
Format for HTML and highlight some interesting regions in different colours: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.3">Go to the output files for this example</a><p><p>
<p>
<b>Example 4</b>
<p>
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  
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.4">Go to the output files for this example</a><p><p>
<p>
<b>Example 5</b>
<p>
Show non-identities between the sequences 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 6</b>
<p>
Show all of the sequences 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.6">Go to the output files for this example</a><p><p>
<p>
<b>Example 7</b>
<p>
Show identities between the sequences 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.7">Go to the output files for this example</a><p><p>
<p>
<b>Example 8</b>
<p>
Show similarities between the sequences 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.8">Go to the output files for this example</a><p><p>
<p>
<b>Example 9</b>
<p>
Show dissimilarities between the sequences 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.9">Go to the output files for this example</a><p><p>
<p>
<b>Example 10</b>
<p>
Use the first sequence as the reference to compare to: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.10">Go to the output files for this example</a><p><p>
<p>
<b>Example 11</b>
<p>
Show a range of sequences in uppercase, everything else in lowercase 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.11">Go to the output files for this example</a><p><p>
<p>
<b>Example 12</b>
<p>
Display the sequences in alphabetic order: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

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

</pre></td></tr></table><p>
<p>
<a href="#output.12">Go to the output files for this example</a><p><p>


<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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

</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>seqset</td>
<td>The sequence alignment to be displayed.</td>
<td>Readable set of sequences</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.showalign</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-matrix</td>
<td>matrix</td>
<td>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.</td>
<td>Comparison matrix file in EMBOSS data path</td>
<td>EBLOSUM62 for protein<br>EDNAFULL for DNA</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-refseq</td>
<td>string</td>
<td>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.</td>
<td>Any string</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]bottom</td>
<td>boolean</td>
<td>If this is true then the reference sequence is displayed at the bottom of the alignment instead of the top.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-show</td>
<td>list</td>
<td>What to show</td>
<td><table><tr><td>A</td> <td><i>(All of the sequences)</i></td></tr><tr><td>I</td> <td><i>(Identities between the sequences)</i></td></tr><tr><td>N</td> <td><i>(Non-identities between the sequences)</i></td></tr><tr><td>S</td> <td><i>(Similarities between the sequences)</i></td></tr><tr><td>D</td> <td><i>(Dissimilarities between the sequences)</i></td></tr></table></td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-order</td>
<td>list</td>
<td>Output order of the sequences</td>
<td><table><tr><td>I</td> <td><i>(Input order - no change)</i></td></tr><tr><td>A</td> <td><i>(Alphabetical order of the names)</i></td></tr><tr><td>S</td> <td><i>(Similarity to the reference sequence)</i></td></tr></table></td>
<td>I</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]similarcase</td>
<td>boolean</td>
<td>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.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]consensus</td>
<td>boolean</td>
<td>If this is true then the consensus line is displayed.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-uppercase</td>
<td>range</td>
<td>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</td>
<td>Sequence range</td>
<td>If this is left blank, then the sequence case is left alone.</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]number</td>
<td>boolean</td>
<td>If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]ruler</td>
<td>boolean</td>
<td>If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed.</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-width</td>
<td>integer</td>
<td>Width of sequence to display</td>
<td>Integer 1 or more</td>
<td>60</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-margin</td>
<td>integer</td>
<td>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.</td>
<td>Integer -1 or more</td>
<td>-1</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-html</td>
<td>boolean</td>
<td>Use HTML formatting</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-highlight</td>
<td>range</td>
<td>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'.</td>
<td>Sequence range</td>
<td><i>full sequence</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-plurality</td>
<td>float</td>
<td>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.</td>
<td>Number from 0.000 to 100.000</td>
<td>50.0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-setcase</td>
<td>float</td>
<td>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.</td>
<td>Any numeric value</td>
<td>@( $(sequence.totweight) / 2)</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-identity</td>
<td>float</td>
<td>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.</td>
<td>Number from 0.000 to 100.000</td>
<td>0.0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]gaps</td>
<td>boolean</td>
<td>If this option is true then gap characters can appear in the consensus. The alternative is 'N' for nucleotide, or 'X' for protein</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-sequence" associated seqset qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sbegin1<br>-sbegin_sequence</td>
<td>integer</td>
<td>Start of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -send1<br>-send_sequence</td>
<td>integer</td>
<td>End of each sequence to be used</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sreverse1<br>-sreverse_sequence</td>
<td>boolean</td>
<td>Reverse (if DNA)</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sask1<br>-sask_sequence</td>
<td>boolean</td>
<td>Ask for begin/end/reverse</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -snucleotide1<br>-snucleotide_sequence</td>
<td>boolean</td>
<td>Sequence is nucleotide</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sprotein1<br>-sprotein_sequence</td>
<td>boolean</td>
<td>Sequence is protein</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -slower1<br>-slower_sequence</td>
<td>boolean</td>
<td>Make lower case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -supper1<br>-supper_sequence</td>
<td>boolean</td>
<td>Make upper case</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -scircular1<br>-scircular_sequence</td>
<td>boolean</td>
<td>Sequence is circular</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -squick1<br>-squick_sequence</td>
<td>boolean</td>
<td>Read id and sequence only</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sformat1<br>-sformat_sequence</td>
<td>string</td>
<td>Input sequence format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -iquery1<br>-iquery_sequence</td>
<td>string</td>
<td>Input query fields or ID list</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ioffset1<br>-ioffset_sequence</td>
<td>integer</td>
<td>Input start position offset</td>
<td>Any integer value</td>
<td>0</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sdbname1<br>-sdbname_sequence</td>
<td>string</td>
<td>Database name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -sid1<br>-sid_sequence</td>
<td>string</td>
<td>Entryname</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -ufo1<br>-ufo_sequence</td>
<td>string</td>
<td>UFO features</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fformat1<br>-fformat_sequence</td>
<td>string</td>
<td>Features format</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fopenfile1<br>-fopenfile_sequence</td>
<td>string</td>
<td>Features file name</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-outfile" associated outfile qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -odirectory2<br>-odirectory_outfile</td>
<td>string</td>
<td>Output directory</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>

<H2>
    Input file format
</H2>

<b>showalign</b> reads in a set of aligned protein or nucleic sequences. 

<p>


<a name="input.1"></a>
<h3>Input files for usage example </h3>
<p><h3>File: globins.msf</h3>
<table width="90%"><tr><td bgcolor="#FFCCFF">
<pre>
!!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~~~

</pre>
</td></tr></table><p>

<p>

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

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

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').
<p>

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 '<FONT COLOR=xxx>'
construct, (where 'xxx' is the name of the colour).
<p>

The standard names of HTML font colours are given in
<A HREF="http://http://www.w3.org/TR/REC-html40/types.html#h-6.5">
http://http://www.w3.org/TR/REC-html40/types.html#h-6.5</A>

<p>

An example highlight range file is:
<p>

<pre>          
# this is my set of ranges
12   23         red
 4   5          darkturquoise
67   10348      #FFE4E1
</pre>
<p>

<H2>
    Output file format
</H2>

<b>showalign</b> writes out a text file, optionally formatted for HTML. 

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                   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

</pre>
</td></tr></table><p>

<a name="output.2"></a>
<h3>Output files for usage example 2</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                   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

</pre>
</td></tr></table><p>

<a name="output.3"></a>
<h3>Output files for usage example 3</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
&lt;pre&gt;
                   10        20        30        40        50        60
           ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN  ---&lt;font color=green&gt;-----VH.tP&lt;/font&gt;E.K.A.TaL.G.V.-VD....E..GR-.L&lt;font color=red&gt;V&lt;/font&gt;vY.WT.R&lt;font color=blue&gt;..Es.G&lt;/font&gt;D..T
HBB_HORSE  ---&lt;font color=green&gt;-----VQ..G&lt;/font&gt;E.KaA.LaL.D.V.-EE....E..GR-.L&lt;font color=red&gt;V&lt;/font&gt;vY.WT.R&lt;font color=blue&gt;..Ds.G&lt;/font&gt;D..N
HBA_HUMAN  ---&lt;font color=green&gt;----------&lt;/font&gt;-VL.PADKTNV.AA-WGk..AH.GEYGAE&lt;font color=red&gt;A&lt;/font&gt;lERMFLS&lt;font color=blue&gt;.PT.KT&lt;/font&gt;YFPH
HBA_HORSE  ---&lt;font color=green&gt;----------&lt;/font&gt;-VL.AADKTNV.AA-WSk...H.GEYGAE&lt;font color=red&gt;A&lt;/font&gt;lERMFLG&lt;font color=blue&gt;.PT.KT&lt;/font&gt;YFPH
MYG_PHYCA  ---&lt;font color=green&gt;----VLSEGE&lt;/font&gt;WqLVLHVWAKVeAd-VAGH.QDI.IR-.F&lt;font color=red&gt;K&lt;/font&gt;SH.ETLE&lt;font color=blue&gt;K.DR.K&lt;/font&gt;H.KT
GLB5_PETMA PIV&lt;font color=green&gt;DTGSVAP..A&lt;/font&gt;A.KtKiR.A.APVYSTY.TS.VDiLVKFF&lt;font color=red&gt;T&lt;/font&gt;ST.AA.E&lt;font color=blue&gt;..PK.K&lt;/font&gt;G.tT
LGB2_LUPLU ---&lt;font color=green&gt;-----GA.tE&lt;/font&gt;SqAaL.K.S.EeF.ANIPKHTHRFFILvL&lt;font color=red&gt;E&lt;/font&gt;.A.AAkD&lt;font color=blue&gt;L.SFLK&lt;/font&gt;GT.E
Consensus  xxx&lt;font color=green&gt;xxxxxxxLSx&lt;/font&gt;xExSxVxSxWxKxNxxxEVGGxALxxxLx&lt;font color=red&gt;x&lt;/font&gt;IxPxxQx&lt;font color=blue&gt;FFxTFx&lt;/font&gt;xLSx

                   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

&lt;/pre&gt;
</pre>
</td></tr></table><p>

<a name="output.4"></a>
<h3>Output files for usage example 4</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
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

</pre>
</td></tr></table><p>

<a name="output.6"></a>
<h3>Output files for usage example 6</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                   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

</pre>
</td></tr></table><p>

<a name="output.7"></a>
<h3>Output files for usage example 7</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                   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

</pre>
</td></tr></table><p>

<a name="output.8"></a>
<h3>Output files for usage example 8</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                   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

</pre>
</td></tr></table><p>

<a name="output.9"></a>
<h3>Output files for usage example 9</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                   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

</pre>
</td></tr></table><p>

<a name="output.10"></a>
<h3>Output files for usage example 10</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                           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

</pre>
</td></tr></table><p>

<a name="output.11"></a>
<h3>Output files for usage example 11</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                           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---

</pre>
</td></tr></table><p>

<a name="output.12"></a>
<h3>Output files for usage example 12</h3>
<p><h3>File: globins.showalign</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
                   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

</pre>
</td></tr></table><p>

<H2>
    Data files
</H2>

<b>showalign</b> reads in scoring matrices to determine the consensus
sequence and to determine which matches are similar or not. 

<p>

<p>
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.

<p>

To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:

<pre>

% embossdata -fetch -file Exxx.dat

</pre>
<p>

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".

<p>
The directories are searched in the following order:

<ul>
   <li> . (your current directory)
   <li> .embossdata (under your current directory)
   <li> ~/ (your home directory)
   <li> ~/.embossdata
</ul>
<p>

<H2>
    Notes
</H2>

<p><b>showalign</b> reads in a scoring matrix to determine the consensus sequence and to determine which matches are similar or not.</p>

<p>By using the <tt>-show</tt> option, the displayed sequences can be shown as:</p>
<ul>
    <li> complete <tt>(-show=All)</tt>,
    <li> only identical matches between the sequence and the reference sequence, all other positions being replaced by '.' characters <tt>(-show=Identities)</tt>
    <li> non-identical matches, with identical matches being replaced by '.' characters, similar matches are shown in lower case <tt>(-show=Non-identities)</tt>
    <li> similar matches, with non-similar matches being replaced by '.' characters, similar matches are shown in lower case <tt>(-show=Similarities)</tt>
    <li> dissimilar matches, with identical or similar matches being replaced by '.' characters <tt>(-show=Dissimilarities)</tt> 
</ul>
<p>Changing the similar matches to lowercase can optionally be disabled by using the option <tt>-nosimilarcase.</tt></p>

<p>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:
<pre>Reference       III

All             ILw
Identical       I..
Non-id          .lW
Similar         Il.
Dissimilar      ..W</pre>
</p>

<p>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 <tt>-setcase</tt>. 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 <tt>-setcase</tt> 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 <tt>-setcase</tt> zero or very large (try 100000 ?). </p>

<p>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.</p>

<p>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.</p>


<H2>
    References
</H2>

None.

<H2>
    Warnings
</H2>

None.

<H2>
    Diagnostic Error Messages
</H2>

None.

<H2>
    Exit status
</H2>

It always exits with status 0.

<H2>
    Known bugs
</H2>

None.


<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="abiview.html">abiview</a></td>
<td>Display the trace in an ABI sequencer file</td>
</tr>

<tr>
<td><a href="coderet.html">coderet</a></td>
<td>Extract CDS, mRNA and translations from feature tables</td>
</tr>

<tr>
<td><a href="edialign.html">edialign</a></td>
<td>Local multiple alignment of sequences</td>
</tr>

<tr>
<td><a href="emma.html">emma</a></td>
<td>Multiple sequence alignment (ClustalW wrapper)</td>
</tr>

<tr>
<td><a href="entret.html">entret</a></td>
<td>Retrieve sequence entries from flatfile databases and files</td>
</tr>

<tr>
<td><a href="extractalign.html">extractalign</a></td>
<td>Extract regions from a sequence alignment</td>
</tr>

<tr>
<td><a href="infoalign.html">infoalign</a></td>
<td>Display basic information about a multiple sequence alignment</td>
</tr>

<tr>
<td><a href="infoseq.html">infoseq</a></td>
<td>Display basic information about sequences</td>
</tr>

<tr>
<td><a href="plotcon.html">plotcon</a></td>
<td>Plot conservation of a sequence alignment</td>
</tr>

<tr>
<td><a href="prettyplot.html">prettyplot</a></td>
<td>Draw a sequence alignment with pretty formatting</td>
</tr>

<tr>
<td><a href="refseqget.html">refseqget</a></td>
<td>Get reference sequence</td>
</tr>

<tr>
<td><a href="seqxref.html">seqxref</a></td>
<td>Retrieve all database cross-references for a sequence entry</td>
</tr>

<tr>
<td><a href="seqxrefget.html">seqxrefget</a></td>
<td>Retrieve all cross-referenced data for a sequence entry</td>
</tr>

<tr>
<td><a href="tranalign.html">tranalign</a></td>
<td>Generate an alignment of nucleic coding regions from aligned proteins</td>
</tr>

<tr>
<td><a href="variationget.html">variationget</a></td>
<td>Get sequence variations</td>
</tr>

<tr>
<td><a href="whichdb.html">whichdb</a></td>
<td>Search all sequence databases for an entry and retrieve it</td>
</tr>

</table>


<H2>
    Author(s)
</H2>
Gary Williams formerly at:
<br>
MRC Rosalind Franklin Centre for Genomics Research
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.

<H2>
    History
</H2>

Written (23 May 2001) - Gary Williams


<H2>
    Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.

<H2>
    Comments
</H2>
None

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