infoalign.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>The sequence alignment to be displayed.</td>
<td>Readable set of sequences</td>
<td><b>Required</b></td>
</tr>

<tr>
<td>[-outfile]<br>(Parameter 2)</td>
<td>If you enter the name of a file here then this program will write the sequence details into that file.</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.infoalign</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>-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>
<td>-refseq</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 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 is accepted</td>
<td>0</td>
</tr>

<tr>
<td>-html</td>
<td>Format output as an HTML table</td>
<td>Boolean value Yes/No</td>
<td>No</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>-plurality</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>
<td>-identity</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>
<td>-only</td>
<td>This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying:
'-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount -noweight'
to get only the sequence length output, you can specify
'-only -seqlength'</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr>
<td>-heading</td>
<td>Display column headings</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-usa</td>
<td>Display the USA of the sequence</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-name</td>
<td>Display 'name' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-seqlength</td>
<td>Display 'seqlength' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-alignlength</td>
<td>Display 'alignlength' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-gaps</td>
<td>Display number of gaps</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-gapcount</td>
<td>Display number of gap positions</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-idcount</td>
<td>Display number of identical positions</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-simcount</td>
<td>Display number of similar positions</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-diffcount</td>
<td>Display number of different positions</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-change</td>
<td>Display % number of changed positions</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-weight</td>
<td>Display 'weight' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

<tr>
<td>-description</td>
<td>Display 'description' column</td>
<td>Boolean value Yes/No</td>
<td>@(!$(only))</td>
</tr>

</table>