This file is indexed.

/usr/share/doc/mcl/html/index.html is in mcl-doc 1:14-137-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
   <html>

   <head>
      <title>MCL manuals</title>
      <style type="text/css">
        body
        { text-align: justify;
          color: #001111;
          background: white;
          margin-left: 8%;
          margin-right: 8%;
        }
        h3 { margin-top:1em; }
        h2 { margin-top:2em; }
      </style>
   </head>

   <body>
   

   
   <hr noshade size=1>
   <h1> MCL user manuals </h1>
   <h3> Installation index 14-137 </h3>
   <hr noshade size=1>
   








   <h3 style="margin-top:2em">Generic stuff</h3>
   <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
   
<tr>
      <td><b>mcl</b> - the mcl manual page</td>
      <td><a href="mcl.html">html</a></td>
      <td><a href="mcl.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mclfaq</b> - the mcl FAQ</td>
      <td><a href="mclfaq.html">html</a></td>
      <td><a href="mclfaq.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcxio</b> - the mcl matrix format specification</td>
      <td><a href="mcxio.html">html</a></td>
      <td><a href="mcxio.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mclpipeline</b> - generic pipeline (parsing/matrix creation/clustering/display)</td>
      <td><a href="mclpipeline.html">html</a></td>
      <td><a href="mclpipeline.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcx</b> - interface to basic matrix operations</td>
      <td><a href="mcx.html">html</a></td>
      <td><a href="mcx.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcxassemble</b> - prepare input matrix from cooccurrence scores</td>
      <td><a href="mcxassemble.html">html</a></td>
      <td><a href="mcxassemble.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcxdump</b> - dump matrices, optionally map indices to labels</td>
      <td><a href="mcxdump.html">html</a></td>
      <td><a href="mcxdump.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcxarray</b> - transform array data to MCL matrices</td>
      <td><a href="mcxarray.html">html</a></td>
      <td><a href="mcxarray.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcxconvert</b> - convert between ascii/binary storage types</td>
      <td><a href="mcxconvert.html">html</a></td>
      <td><a href="mcxconvert.ps">ps</a></td>
   </tr>
</table>



   <h3 style="margin-top:2em">Dealing with clustering results</h3>
   <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
   
<tr>
      <td><b>clmformat</b> - display clusterings in browsable format</td>
      <td><a href="clmformat.html">html</a></td>
      <td><a href="clmformat.ps">ps</a></td>
   </tr>
<tr>
      <td><b>clmdist</b> - compute distances between clusterings</td>
      <td><a href="clmdist.html">html</a></td>
      <td><a href="clmdist.ps">ps</a></td>
   </tr>
<tr>
      <td><b>clminfo</b> - performance measures for clusterings</td>
      <td><a href="clminfo.html">html</a></td>
      <td><a href="clminfo.ps">ps</a></td>
   </tr>
<tr>
      <td><b>clmmeet</b> - compute intersection of clusterings</td>
      <td><a href="clmmeet.html">html</a></td>
      <td><a href="clmmeet.ps">ps</a></td>
   </tr>
<tr>
      <td><b>clmmate</b> - compute best matches between two clusterings</td>
      <td><a href="clmmate.html">html</a></td>
      <td><a href="clmmate.ps">ps</a></td>
   </tr>
<tr>
      <td><b>clmimac</b> - Interpret Matrices (c.q. MCL iterands) As Clusterings</td>
      <td><a href="clmimac.html">html</a></td>
      <td><a href="clmimac.ps">ps</a></td>
   </tr>
<tr>
      <td><b>clmresidue</b> - extend subgraph clusterings onto encompassing graph</td>
      <td><a href="clmresidue.html">html</a></td>
      <td><a href="clmresidue.ps">ps</a></td>
   </tr>
<tr>
      <td><b>clmorder</b> - reorder indices to represent blocks from different clusterings</td>
      <td><a href="clmorder.html">html</a></td>
      <td><a href="clmorder.ps">ps</a></td>
   </tr>
<tr>
      <td><b>clmclose</b> - fetch connected components from graphs or subgraphs</td>
      <td><a href="clmclose.html">html</a></td>
      <td><a href="clmclose.ps">ps</a></td>
   </tr>
</table>



   <h3 style="margin-top:2em">Dealing with matrices</h3>
   <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
   
<tr>
      <td><b>mcxio</b> - the mcl matrix format specification</td>
      <td><a href="mcxio.html">html</a></td>
      <td><a href="mcxio.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcx</b> - interface to basic matrix operations</td>
      <td><a href="mcx.html">html</a></td>
      <td><a href="mcx.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcxsubs</b> - extract submatrices by specifiying sets of nodes and clusters</td>
      <td><a href="mcxsubs.html">html</a></td>
      <td><a href="mcxsubs.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcxmap</b> - remap matrix indices / relabel graph nodes</td>
      <td><a href="mcxmap.html">html</a></td>
      <td><a href="mcxmap.ps">ps</a></td>
   </tr>
<tr>
      <td><b>mcxassemble</b> - prepare input matrix from cooccurrence scores</td>
      <td><a href="mcxassemble.html">html</a></td>
      <td><a href="mcxassemble.ps">ps</a></td>
   </tr>
</table>



   <h3 style="margin-top:2em">Application specific parsers and wrappers</h3>
   <table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
   
   <tr>
      <th colspan="3">
      <b>BLAST package</b> - Documentation only available if installed with <b>--enable-blast</b>
      </th>
   </tr>
   
   <tr>
      <td><b>mclblastline</b> - pipeline for clustering from blast files</td>
      <td><a href="mclblastline.html">html</a></td>
      <td><a href="mclblastline.ps">ps</a></td>
   </tr>
   <tr>
      <td><b>mcxdeblast</b> - prepare input from blast files</td>
      <td><a href="mcxdeblast.html">html</a></td>
      <td><a href="mcxdeblast.ps">ps</a></td>
   </tr>
</table>


</body>
</html>