cons.itable

emboss的linux版本的源代码

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>File containing a sequence alignment.</td>
<td>Readable set of sequences</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>[-outseq]<br>(Parameter 2)</td>
<td>Sequence filename and optional format (output USA)</td>
<td>Writeable sequence</td>
<td><i>&lt;*&gt;</i>.<i>format</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td>-datafile</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>
<td>-plurality</td>
<td>Set a cut-off for the number of positive matches below which there is no consensus. The default plurality is taken as half the total weight of all the sequences in the alignment.</td>
<td>Any numeric value</td>
<td>Half the total sequence weighting</td>
</tr>

<tr>
<td>-identity</td>
<td>Provides the facility of setting the required number of identities at a site for it to give a consensus at that position. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus.</td>
<td>Integer 0 or more</td>
<td>0</td>
</tr>

<tr>
<td>-setcase</td>
<td>Sets the threshold for the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case.</td>
<td>Any numeric value</td>
<td>@( $(sequence.totweight) / 2)</td>
</tr>

<tr>
<td>-name</td>
<td>Name of the consensus sequence</td>
<td>Any string is accepted</td>
<td><i>An empty string is accepted</i></td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr>
<td colspan=4>(none)</td>
</tr>

</table>