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<?xml version="1.0" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>alifmt</title>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
</head>
<body style="background-color: white">
<!-- INDEX BEGIN -->
<div name="index">
<p><a name="__index__"></a></p>
<!--
<ul>
<li><a href="#name">NAME</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#see_also">SEE ALSO</a></li>
<li><a href="#author">AUTHOR</a></li>
</ul>
-->
</div>
<!-- INDEX END -->
<p>This document illustrates some common formats used for aligned sequences
representation.</p>
<dl>
<dt><strong><a name="clustal" class="item"><strong>CLUSTAL</strong></a></strong></dt>
<dd>
<pre>
CLUSTAL W (1.82) multiple sequence alignment</pre>
<pre>
MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTL
MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTL
MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTL
MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------
*:** *:**:**:*:.::**:***:*::***</pre>
<pre>
MALK_ECOLI LRMIAGLETITSGDLACRRLHKEPGV
MALK_SALTY LRMIAGLETITSGDLACRRLHQEPGV
MALK_ENTAE LRMIAGLETVTSGDL-----------
MALK_PHOLU LRM-----------------------
***</pre>
<p><strong>Warning</strong>: Names must not contain spaces or exceed 30 characters.</p>
</dd>
<dt><strong><a name="fasta" class="item"><strong>FASTA</strong></a></strong></dt>
<dd>
<pre>
>MALK_ECOLI
MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
GLETITSGDLACRRLHKEPGV
>MALK_SALTY
MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
GLETITSGDLACRRLHQEPGV
>MALK_ENTAE
MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
GLETVTSGDL-----------
>MALK_PHOLU
MSSVTLRNVSKAYGETIISKNINLEIQEGEF--------------LRM--
---------------------</pre>
</dd>
<dt><strong><a name="mega" class="item"><strong>MEGA</strong></a></strong></dt>
<dd>
<pre>
#mega
!Title Multiple Sequence Alignment;</pre>
<pre>
#MALK_ECOLI
MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
GLETITSGDLACRRLHKEPGV
#MALK_SALTY
MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
GLETITSGDLACRRLHQEPGV
#MALK_ENTAE
MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
GLETVTSGDL-----------
#MALK_PHOLU
MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------
---------------------</pre>
</dd>
<dt><strong><a name="msf" class="item"><strong>MSF</strong></a></strong></dt>
<dd>
<pre>
!!AA_MULTIPLE_ALIGNMENT 1.0
PileUp of: @pep.list</pre>
<pre>
msf.seq MSF: 55 Type: P Nov 22, 2001 11:02 Check: 2529 ..</pre>
<pre>
Name: m73237 Len: 655 Check: 7493 Weight: 1.00
Name: l28824 Len: 655 Check: 5456 Weight: 1.00
Name: u04379 Len: 655 Check: 9580 Weight: 1.00</pre>
<pre>
//</pre>
<pre>
1 50
m73237 ~~~~~MADSA NHLPFFFGQI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
l28824 MASSGMADSA NHLPFFFGNI TREEAEDYLV QGGMSDGLYL LRQSRNYLGG
u04379 ~~~~~MPDPA AHLPFFYGSI SRAEAEEHLK LAGMADGLFL LRQCLRSLGG</pre>
<pre>
51
m73237 ~~~~~
l28824 ~~~~~
u04379 AACG*</pre>
<p><strong>Warning</strong>: This format cannot handle more than 500 sequences in a
single alignment.</p>
</dd>
<dt><strong><a name="nexus" class="item"><strong>NEXUS</strong></a></strong></dt>
<dd>
<pre>
#NEXUS</pre>
<pre>
begin data;
dimensions ntax=2 nchar=80;
format datatype=Protein interleave gap=- missing='.';
matrix
[ 1 50]
btdDm -------AQQQQHHLHMQQAQHH-----------LHLSH------QQAQQ
TSp1 --------------------AEH-----------PSLR--------GTPL</pre>
<pre>
[ 51 80]
btdDm YACPICSKKFSRSDHLSKHKKTHF------
TSp1 FACPICNKRFMRSDHLAKHVKTHN------</pre>
<pre>
;
endblock;</pre>
<p><strong>Warning</strong>: Text enclosed in brackets is considered as comment, and
thus ignored.</p>
</dd>
<dt><strong><a name="phylip" class="item"><strong>PHYLIP</strong></a></strong></dt>
<dd>
<p>Sequential (PHYLIPS):</p>
<pre>
2 109
ATISA1 GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENNDG
ENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMGDE
YGHTKGGN---
POTISA1 GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKDG
ENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMGDE
YGHTKGGN---</pre>
<p>Interleaved (PHYLIPI):</p>
<pre>
2 109
ATISA1 GSPNLYQ-GGRKPWHSINFICAHDGFTLADLVTYNNKNNLANGEENND
POTISA1 GSPNLYQKGGRKPWNSINFVCAHDGFTLADLVTYNNKHNLANGEDNKD</pre>
<pre>
GENHNYSWNCGEEGDFASISVKRLRKRQMRNFFVSLMVSQGVPMIYMG
GENHNNSWNCGEEGEFASIFVKKLRKRQMRNFFLCLMVSQGVPMIYMG</pre>
<pre>
DEYGHTKGGN---
DEYGHTKGGN---</pre>
<p><strong>Warning</strong>: Species names may not contain characters `( ) : ; , [ ]'
and exceed 10 characters.</p>
</dd>
<dt><strong><a name="stockholm" class="item"><strong>STOCKHOLM</strong></a></strong></dt>
<dd>
<pre>
# STOCKHOLM 1.0</pre>
<pre>
MALK_ECOLI MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIA
MALK_SALTY MASVQLRNVTKAWGDVVVSKDINLDIHDGEFVVFVGPSGCGKSTLLRMIA
MALK_ENTAE MASVQLRNVTKAWGDVVVSKDINLEIQDGEFVVFVGPSGCGKSTLLRMIA
MALK_PHOLU MSSVTLRNVSKAYGETIISKNINLEIQEGEF-------------------</pre>
<pre>
MALK_ECOLI RCHLFREDGTACRRLHKEPGV
MALK_SALTY RCHLFREDGSACRRLHQEPGV
MALK_ENTAE ---------------------
MALK_PHOLU ---------------------
//</pre>
</dd>
</dl>
</body>
</html>
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