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<html>
<head>
<title>
T-Coffee: A Consistency Based Multiple Alignmnent Method Multiple Alignments (Notredame,Higgins, Heringa)
</title>
</head>
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<FORM enctype="multipart/form-data" method="POST" ACTION="t_coffee4html.cgi">
<INPUT NAME="simple" TYPE="HIDDEN" VALUE="yes">
<INPUT NAME="Title" TYPE="HIDDEN" VALUE="T-Coffee Multiple Alignments (Notredame, Higgins,Heringa)">
<INPUT NAME="Cmd" TYPE="HIDDEN" VALUE="T-Coffee">
<INPUT NAME="-maxnseq" TYPE="HIDDEN" VALUE="30">
<INPUT NAME="-maxlen" TYPE="HIDDEN" VALUE="400">
</head>
<!---TITLE--->
<body bgcolor=#FFFFFF>
<table bgcolor="#FFFFFF" border="8" cellpadding="8" align=center width=60%>
<tr>
<td align=center>
<h1><a href="http://mathbio.nimr.mrc.ac.uk/~cnotred/">T-Coffee</h1></a>
<h2> A Tool For Multiple Sequence Alignments</h2>
<h4>Notredame, Higgins, Heringa</h4>
</td>
</tr>
</table>
<h4></h4>
<h4 align=left font=12>T-Coffee will combine together
several alignments. By default, T-Coffee will generate the 20 best local
alignments (lalign) and the best global alignment for each pair of
sequences. It will then combine all this information into one multiple
sequence alignment. If you request it
(<a href="#Methods">Methods</a>), T-Coffee can also generate and combine
several multiple alignments using the most common methods (prrp, pima,
dialign...), or use your own multiple sequence alignmnents (<a
href="#Data Input">Data Input</a>).</h4>
<!--Start of the sumbmission form table--->
<table bgcolor="#EEEEFF" border="8" cellspacing="8"
cellpadding="8"align=center width=95%>
<!---HELP--->
<tr>
<td align=center>
<h2 align=left font=12>For a default utilisation, simply paste or upload your
sequences in the box 1 on Data Input and press the run button <font
color=red> (Limit: 20 sequences 300 residues)</font></h2>
<table border=2 bgcolor=#AE7777 align=center width=25% >
<tr><td> <INPUT TYPE="reset" VALUE="Reset"></td><td><INPUT TYPE="submit"
VALUE="Run T-Coffee"></tr></td>
</table>
</td>
</tr>
<!---INPUT OF THE EXPERIENCE NAME--->
<tr>
<td>
<h1 align=center>Labelling</h1>
<table border=0 cellpading=0 >
<H4>
<tr>
<td>Type in the name of your alignment</td>
<td><INPUT TYPE="text" VALUE="t_coffee" NAME="run_name"></td>
</tr>
<tr>
<td> <font color=red>Your e-mail</font></td>
<td><INPUT TYPE="text" VALUE="" NAME="e-mail"></td>
</tr>
<tr>
<td> Results</h4></td>
<td>
<SELECT NAME="result_mode">
<OPTION SELECTED VALUE="online"> ON LINE </OPTION>
<OPTION VALUE="mail"> BY EMAIL</OPTION>
</SELECT>
</td>
</tr>
</H4>
</table>
</td>
</tr>
<!---INPUT OF THE DATA--->
<tr>
<td>
<h1 align=center><a name="Data Input"></a><a href="t_coffee_doc.html#FORMATS">Data Input</a><h1>
<h2 align=left ><a href="t_coffee_doc.html#A Sequences">Sequences</a>,
<a href="t_coffee_doc.html#B ALignments">Alignments </a> or
<a href="t_coffee_doc.html#C Libraries"> Libraries</a></h2>
<h2 align=left >In each field, input<a href="t_coffee_doc.html#-in"> either</a> a set of sequences, a
multiple alignment or a library. All the fields do not need to be to be filled.</h2>
<table bgcolor="white" border="1" cellpadding="1" align=left width=80%>
<tr>
<td align=center bgcolor=#EAEAAE><H4>1</H4></td>
<td align=center><H4>input a File Name <INPUT TYPE="file"
NAME="-in"><SPACE SIZE=15> or Paste <TEXTAREA NAME = "data" ROWS =1 COLS = 50></TEXTAREA></H4></td>
</tr>
<tr>
<td align=center bgcolor=#EAEAAE><H4>2</H4></td>
<td align=center><H4>input a file Name <INPUT TYPE="file" NAME="-in"><SPACE SIZE=15>
or Paste <TEXTAREA NAME = "data" ROWS =1 COLS = 50></TEXTAREA></H4></td>
</tr>
<tr>
<td align=center bgcolor=#EAEAAE><H4>3</H4></td>
<td align=center><H4>input a file Name <INPUT TYPE="file" NAME="-in"><SPACE SIZE=15>
or Paste <TEXTAREA NAME = "data" ROWS =1 COLS = 50></TEXTAREA></H4></td>
</tr>
<tr>
<td align=center bgcolor=#EAEAAE><H4>4</H4></td>
<td align=center><H4>input a file Name <INPUT TYPE="file" NAME="-in"><SPACE SIZE=15>
or Paste <TEXTAREA NAME = "data" ROWS =1 COLS = 50></TEXTAREA></H4></td>
</tr>
<tr>
<td align=center bgcolor=#EAEAAE><H4>5</H4></td>
<td align=center><H4>input a file Name <INPUT TYPE="file" NAME="-in"><SPACE SIZE=15>
or Paste <TEXTAREA NAME = "data" ROWS =1 COLS = 50></TEXTAREA></H4></td>
</tr>
</table>
</td>
</tr>
<!---OUTPUT OF THE DATA--->
<tr>
<td> <h1 align=center>Data Output</h1>
<h2 align=left> Check the<a href="t_coffee_doc.html#-output"> format</a> you wish to produce </h2>
<table bgcolor=white border="1" cellpadding="1" align="left" width=80%>
<tr>
<td rowspan=2 bgcolor=#EAEAAE ><H4>Alignment Format</H4></td>
<td><H4><INPUT TYPE="checkbox" NAME="-output" VALUE="msf_aln">msf</H4></td>
<td><H4><INPUT TYPE="checkbox" CHECKED NAME="-output" VALUE="clustalw" >clustalw</H4></td>
<td><H4><INPUT TYPE="checkbox" NAME="-output" VALUE="fasta_aln">fasta</H4></td>
</tr>
<tr>
<td><H4><INPUT TYPE="checkbox" CHECKED NAME="-output" value="score_html"> color (html)</H4></td>
<td><H4><INPUT TYPE="checkbox" NAME="-output" VALUE="score_ps"> color (ps)</H4></td>
<td><H4><INPUT TYPE="checkbox" NAME="-output" VALUE="score_pdf"> color (pdf)</H4></td>
</tr>
</table>
</td>
</tr>
<!---CHOICE OF THE METHODS--->
<tr>
<td>
<h1 align=center><a name="Methods">Methods</a></h1>
<h2 align=left> Check the methods you wish to use </h2>
<table bgcolor=white border="1" cellpadding="1" align="left" width=80%>
<tr>
<td bgcolor=#EAEAAE ><H4><a href="t_coffee_doc.html#-matrix"> Substitution Matrix</a></H4></td>
<td>
<SELECT NAME="-in">
<OPTION SELECTED VALUE="">-no matrix-</OPTION>
<OPTION VALUE="blosum62mt"> BLOSUM 62 </OPTION>
<OPTION VALUE="pam250mt"> PAM 250</OPTION>
<OPTION VALUE="idmat"> identity </OPTION>
</SELECT>
</td>
<td align=center colspan=2><font color=red> WARNING: if you select a
matrix, NO OTHER method will be used </font></td>
<tr>
<td bgcolor=#EAEAAE rowspan=2 ><H4><a href="t_coffee_doc.html#Existing Methods"> Pairwise Methods</a></H4></td>
<td><h4><INPUT TYPE="checkbox" CHECKED NAME="-in"
value="lalign_id_pair"><a href="t_coffee_doc.html#lalign_pair"> lalign</a>(pair)</H4></td>
<td><h4><INPUT TYPE="checkbox" NAME="-in"
value="clustalw_pair"><a href="t_coffee_doc.html#clustalw_pair"> clustalw</a>(pair)</H4></td>
<td><h4><INPUT TYPE="checkbox" CHECKED NAME="-in"
value="fast_pair"><a href="t_coffee_doc.html#fast_pair"> fast</a>(pair)</H4></td>
</tr>
<tr>
<td><h4><INPUT TYPE="checkbox" NAME="-in"
value="cfast_pair"><a href="t_coffee_doc.html#cfast_pair"> checked fast</a>(pair)</H4></td>
<td><h4> </td>
<td><h4> </td>
</tr>
<tr>
<td bgcolor=#EAEAAE rowspan=2 ><H4><a href="t_coffee_doc.html#Existing Methods"> Multiple Aln Methods</a></H4></td>
<td><h4><INPUT TYPE="checkbox" NAME="-in"
value="clustalw_aln"><a href="t_coffee_doc.html#clustalw_aln"> clustalw</a></H4></td>
<td><h4><INPUT TYPE="checkbox" NAME="-in"
value="prrp_aln"><a href="t_coffee_doc.html#clustalw_aln"> prrp</a></H4></td>
<!---
<td><h4><INPUT TYPE="checkbox" NAME="-in"
value="dialign_aln"><a href="t_coffee_doc.html#clustalw_aln"> dialign</a></H4></td>
</tr>
<tr>
<td><h4><INPUT TYPE="checkbox" NAME="-in"
value="dca_aln"><a href="t_coffee_doc.html#clustalw_aln"> dca</a></H4></td>
<td><h4><INPUT TYPE="checkbox" NAME="-in"
value="pima_aln"><a href="t_coffee_doc.html#clustalw_aln">
pima</a></H4></td>
--->
<td><h4> </td>
</tr>
</table>
</td>
</tr>
<!---PARAMETERS--->
<tr>
<td>
<h1 align=center>Extended Parameters</h1>
<table bgcolor=white border="1" cellpadding="1" align="left" width=80%>
<tr>
<td rowspan=3 bgcolor=#EAEAAE ><H4>Multiple Aln</H4></td>
<td><h4 align=center><a href="t_coffee_doc.html#-gapopen"> gapopen</a></h4><h4 align=center> <INPUT align=right TYPE="text" VALUE="0" NAME="-gapopen" size=4></h4></td>
<td><h4 align=center><a href="t_coffee_doc.html#-gapext"> gapext</a></h4><h4 align=center><INPUT align=right TYPE="text" VALUE="0" NAME="-gapext" size=4></h4></td>
<td><h4 align=center><a href="t_coffee_doc.html#-cosmetic_penalty"> cosmetic penalty</a></h4><h4 align=center><INPUT TYPE="text" VALUE="-100" NAME="-cosmetic_penalty" size=4></h4></td>
</tr>
<tr>
<td><h4 align=center><a href="t_coffee_doc.html#-tg_mode"> terminal gap</a>
<SELECT NAME="-tg_mode"></h4><h4 align=center>
<OPTION VALUE="0">gapopen and gapext</OPTION>
<OPTION SELECTED VALUE="1">gapopen only</OPTION>
<OPTION VALUE="2">no penalty</OPTION>
</SELECT>
</H4>
</td>
<td><h4 align=center><a href="t_coffee_doc.html#-dp_mode"> dp mode</a></h4><h4 align=center>
<SELECT NAME="-dp_mode">
<OPTION VALUE="gotoh_">gotoh_pair_wise</OPTION>
<OPTION VALUE="myers_miller_pair_wise">myers_miller_pair_wise</OPTION>
<OPTION VALUE="fasta_pair_wise">fasta_pair_wise</OPTION>
<OPTION SELECTED VALUE="cfasta_pair_wise">cfasta_pair_wise</OPTION>
</SELECT>
</H4>
</td>
<td><h4 align=center><a href="t_coffee_doc.html#-do_normalise"> normalise</a></h4><h4 align=center>
<INPUT align=right TYPE="text" VALUE="1000"
NAME="-do_normalise" size=4></h4>
</td>
</tr>
<tr>
<td><h4 align=center><a href="t_coffee_doc.html#-usetree"> your tree</a></h4><h4 align=center><INPUT TYPE="file" NAME="-usetree"></h4></td>
<td><h4 align=center><a href="t_coffee_doc.html#-tree_mode"> tree
computation</a></h4><h4 align=center>
<SELECT NAME="-tree_mode">
<OPTION VALUE="slow">slow</OPTION>
<OPTION SELECTED VALUE="fast">fast</OPTION>
<OPTION VALUE="slow">very_fast</OPTION>
</SELECT>
</H4>
</td>
<td> </td>
</tr>
<tr>
<td rowspan=2 bgcolor=#EAEAAE ><H4>Fasta_pair_wise</H4></td>
<td><h4 align=center><a href="t_coffee_doc.html#-ktuple"> ktuple</a></h4><h4 align=center>
<SELECT NAME="-ktuple">
<OPTION SELECTED VALUE="1">1</OPTION>
<OPTION VALUE="2">2</OPTION>
<OPTION VALUE="3">3</OPTION>
<OPTION VALUE="4">4</OPTION>
</SELECT>
</H4>
</td>
<td><h4 align=center><a href="t_coffee_doc.html#-ndiag"> ndiag</a> </h4><h4 align=center><INPUT align=right TYPE="text" VALUE="0" NAME="-ndiag" size=4></h4></td>
<td><h4 align=center><a href="t_coffee_doc.html#-diag_mode"> diag evaluation</a></h4><h4 align=center>
<SELECT NAME="-diag_mode">
<OPTION SELECTED VALUE="0">complete diag</OPTION>
<OPTION VALUE="1">best segment</OPTION>
</SELECT>
</H4>
</td>
</tr>
<tr>
<td><h4 align=center><a href="t_coffee_doc.html#-sim_matrix"> similarity matrix</a></h4><h4 align=center>
<SELECT NAME="-sim_matrix">
<OPTION SELECTED VALUE="vasiliky">vasiliky</OPTION>
<OPTION VALUE="clustalw_col">clustalw_col</OPTION>
<OPTION VALUE="clustalw_dot">clustalw_dot</OPTION>
<OPTION VALUE="idmat">idmat</OPTION>
</SELECT>
</H4>
</td>
<td> </td>
<td> </td>
</tr>
<tr>
<td bgcolor=#EAEAAE ><H4>Output</H4></td>
<td><h4 align=center><a href="t_coffee_doc.html#-outorder"> output order</a></h4><h4 align=center>
<SELECT NAME="-outorder">
<OPTION SELECTED VALUE="aligned">aligned</OPTION>
<OPTION VALUE="input">input</OPTION>
</SELECT>
</h4>
</td>
<td><h4 align=center ><a href="t_coffee_doc.html#-seqnos"> Residue Number</a></h4><h4 align=center>
<SELECT NAME="-seqnos">
<OPTION SELECTED VALUE="off">off</OPTION>
<OPTION VALUE="on">on</OPTION>
</SELECT>
</h4>
</td>
<td><h4 align=center ><a href="t_coffee_doc.html#-case"> Case</a></h4><h4 align=center>
<SELECT NAME="-case">
<OPTION SELECTED VALUE="upper">upper</OPTION>
<OPTION VALUE="lower">lower</OPTION>
</SELECT>
</h4>
</td>
</tr>
</table>
</td>
</tr>
<!---RUN II--->
<tr>
<td align=center>
<table border=2 bgcolor=#AE7777 align=center width=25% >
<tr><td> <INPUT TYPE="reset" VALUE="Reset"></td><td><INPUT TYPE="submit"
VALUE="Run T-Coffee"></tr></td>
</table>
</td>
</tr>
<!---END OF THE FORM--->
</table>
<!---COPYRIGHT--->
<h2>This page was produced by Cedric Notredame
(<a href="mailto:Cedric.notredame@europe.com">Cedric.notredame@europe.com</a>)</h2>
<h2>Please do not hesitate to send me any feed back you may feel appropriate</h2>
<!--END-->
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