1<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff"> 2<tr bgcolor="#FFFFCC"> 3<th align="left">Qualifier</th> 4<th align="left">Type</th> 5<th align="left">Description</th> 6<th align="left">Allowed values</th> 7<th align="left">Default</th> 8</tr> 9 10<tr bgcolor="#FFFFCC"> 11<th align="left" colspan=5>Standard (Mandatory) qualifiers</th> 12</tr> 13 14<tr bgcolor="#FFFFCC"> 15<td>[-sequence]<br>(Parameter 1)</td> 16<td>seqset</td> 17<td>File containing a sequence alignment.</td> 18<td>Readable set of sequences</td> 19<td><b>Required</b></td> 20</tr> 21 22<tr bgcolor="#FFFFCC"> 23<td>[-outseq]<br>(Parameter 2)</td> 24<td>seqout</td> 25<td>Sequence filename and optional format (output USA)</td> 26<td>Writeable sequence</td> 27<td><i><*></i>.<i>format</i></td> 28</tr> 29 30<tr bgcolor="#FFFFCC"> 31<th align="left" colspan=5>Additional (Optional) qualifiers</th> 32</tr> 33 34<tr bgcolor="#FFFFCC"> 35<td>-datafile</td> 36<td>matrix</td> 37<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> 38<td>Comparison matrix file in EMBOSS data path</td> 39<td>EBLOSUM62 for protein<br>EDNAFULL for DNA</td> 40</tr> 41 42<tr bgcolor="#FFFFCC"> 43<td>-plurality</td> 44<td>float</td> 45<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> 46<td>Any numeric value</td> 47<td>Half the total sequence weighting</td> 48</tr> 49 50<tr bgcolor="#FFFFCC"> 51<td>-identity</td> 52<td>integer</td> 53<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> 54<td>Integer 0 or more</td> 55<td>0</td> 56</tr> 57 58<tr bgcolor="#FFFFCC"> 59<td>-setcase</td> 60<td>float</td> 61<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> 62<td>Any numeric value</td> 63<td>@( $(sequence.totweight) / 2)</td> 64</tr> 65 66<tr bgcolor="#FFFFCC"> 67<td>-name</td> 68<td>string</td> 69<td>Name of the consensus sequence</td> 70<td>Any string</td> 71<td> </td> 72</tr> 73 74<tr bgcolor="#FFFFCC"> 75<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th> 76</tr> 77 78<tr> 79<td colspan=5>(none)</td> 80</tr> 81 82<tr bgcolor="#FFFFCC"> 83<th align="left" colspan=5>Associated qualifiers</th> 84</tr> 85 86<tr bgcolor="#FFFFCC"> 87<td align="left" colspan=5>"-sequence" associated seqset qualifiers 88</td> 89</tr> 90 91<tr bgcolor="#FFFFCC"> 92<td> -sbegin1<br>-sbegin_sequence</td> 93<td>integer</td> 94<td>Start of each sequence to be used</td> 95<td>Any integer value</td> 96<td>0</td> 97</tr> 98 99<tr bgcolor="#FFFFCC"> 100<td> -send1<br>-send_sequence</td> 101<td>integer</td> 102<td>End of each sequence to be used</td> 103<td>Any integer value</td> 104<td>0</td> 105</tr> 106 107<tr bgcolor="#FFFFCC"> 108<td> -sreverse1<br>-sreverse_sequence</td> 109<td>boolean</td> 110<td>Reverse (if DNA)</td> 111<td>Boolean value Yes/No</td> 112<td>N</td> 113</tr> 114 115<tr bgcolor="#FFFFCC"> 116<td> -sask1<br>-sask_sequence</td> 117<td>boolean</td> 118<td>Ask for begin/end/reverse</td> 119<td>Boolean value Yes/No</td> 120<td>N</td> 121</tr> 122 123<tr bgcolor="#FFFFCC"> 124<td> -snucleotide1<br>-snucleotide_sequence</td> 125<td>boolean</td> 126<td>Sequence is nucleotide</td> 127<td>Boolean value Yes/No</td> 128<td>N</td> 129</tr> 130 131<tr bgcolor="#FFFFCC"> 132<td> -sprotein1<br>-sprotein_sequence</td> 133<td>boolean</td> 134<td>Sequence is protein</td> 135<td>Boolean value Yes/No</td> 136<td>N</td> 137</tr> 138 139<tr bgcolor="#FFFFCC"> 140<td> -slower1<br>-slower_sequence</td> 141<td>boolean</td> 142<td>Make lower case</td> 143<td>Boolean value Yes/No</td> 144<td>N</td> 145</tr> 146 147<tr bgcolor="#FFFFCC"> 148<td> -supper1<br>-supper_sequence</td> 149<td>boolean</td> 150<td>Make upper case</td> 151<td>Boolean value Yes/No</td> 152<td>N</td> 153</tr> 154 155<tr bgcolor="#FFFFCC"> 156<td> -scircular1<br>-scircular_sequence</td> 157<td>boolean</td> 158<td>Sequence is circular</td> 159<td>Boolean value Yes/No</td> 160<td>N</td> 161</tr> 162 163<tr bgcolor="#FFFFCC"> 164<td> -squick1<br>-squick_sequence</td> 165<td>boolean</td> 166<td>Read id and sequence only</td> 167<td>Boolean value Yes/No</td> 168<td>N</td> 169</tr> 170 171<tr bgcolor="#FFFFCC"> 172<td> -sformat1<br>-sformat_sequence</td> 173<td>string</td> 174<td>Input sequence format</td> 175<td>Any string</td> 176<td> </td> 177</tr> 178 179<tr bgcolor="#FFFFCC"> 180<td> -iquery1<br>-iquery_sequence</td> 181<td>string</td> 182<td>Input query fields or ID list</td> 183<td>Any string</td> 184<td> </td> 185</tr> 186 187<tr bgcolor="#FFFFCC"> 188<td> -ioffset1<br>-ioffset_sequence</td> 189<td>integer</td> 190<td>Input start position offset</td> 191<td>Any integer value</td> 192<td>0</td> 193</tr> 194 195<tr bgcolor="#FFFFCC"> 196<td> -sdbname1<br>-sdbname_sequence</td> 197<td>string</td> 198<td>Database name</td> 199<td>Any string</td> 200<td> </td> 201</tr> 202 203<tr bgcolor="#FFFFCC"> 204<td> -sid1<br>-sid_sequence</td> 205<td>string</td> 206<td>Entryname</td> 207<td>Any string</td> 208<td> </td> 209</tr> 210 211<tr bgcolor="#FFFFCC"> 212<td> -ufo1<br>-ufo_sequence</td> 213<td>string</td> 214<td>UFO features</td> 215<td>Any string</td> 216<td> </td> 217</tr> 218 219<tr bgcolor="#FFFFCC"> 220<td> -fformat1<br>-fformat_sequence</td> 221<td>string</td> 222<td>Features format</td> 223<td>Any string</td> 224<td> </td> 225</tr> 226 227<tr bgcolor="#FFFFCC"> 228<td> -fopenfile1<br>-fopenfile_sequence</td> 229<td>string</td> 230<td>Features file name</td> 231<td>Any string</td> 232<td> </td> 233</tr> 234 235<tr bgcolor="#FFFFCC"> 236<td align="left" colspan=5>"-outseq" associated seqout qualifiers 237</td> 238</tr> 239 240<tr bgcolor="#FFFFCC"> 241<td> -osformat2<br>-osformat_outseq</td> 242<td>string</td> 243<td>Output seq format</td> 244<td>Any string</td> 245<td> </td> 246</tr> 247 248<tr bgcolor="#FFFFCC"> 249<td> -osextension2<br>-osextension_outseq</td> 250<td>string</td> 251<td>File name extension</td> 252<td>Any string</td> 253<td> </td> 254</tr> 255 256<tr bgcolor="#FFFFCC"> 257<td> -osname2<br>-osname_outseq</td> 258<td>string</td> 259<td>Base file name</td> 260<td>Any string</td> 261<td> </td> 262</tr> 263 264<tr bgcolor="#FFFFCC"> 265<td> -osdirectory2<br>-osdirectory_outseq</td> 266<td>string</td> 267<td>Output directory</td> 268<td>Any string</td> 269<td> </td> 270</tr> 271 272<tr bgcolor="#FFFFCC"> 273<td> -osdbname2<br>-osdbname_outseq</td> 274<td>string</td> 275<td>Database name to add</td> 276<td>Any string</td> 277<td> </td> 278</tr> 279 280<tr bgcolor="#FFFFCC"> 281<td> -ossingle2<br>-ossingle_outseq</td> 282<td>boolean</td> 283<td>Separate file for each entry</td> 284<td>Boolean value Yes/No</td> 285<td>N</td> 286</tr> 287 288<tr bgcolor="#FFFFCC"> 289<td> -oufo2<br>-oufo_outseq</td> 290<td>string</td> 291<td>UFO features</td> 292<td>Any string</td> 293<td> </td> 294</tr> 295 296<tr bgcolor="#FFFFCC"> 297<td> -offormat2<br>-offormat_outseq</td> 298<td>string</td> 299<td>Features format</td> 300<td>Any string</td> 301<td> </td> 302</tr> 303 304<tr bgcolor="#FFFFCC"> 305<td> -ofname2<br>-ofname_outseq</td> 306<td>string</td> 307<td>Features file name</td> 308<td>Any string</td> 309<td> </td> 310</tr> 311 312<tr bgcolor="#FFFFCC"> 313<td> -ofdirectory2<br>-ofdirectory_outseq</td> 314<td>string</td> 315<td>Output directory</td> 316<td>Any string</td> 317<td> </td> 318</tr> 319 320<tr bgcolor="#FFFFCC"> 321<th align="left" colspan=5>General qualifiers</th> 322</tr> 323 324<tr bgcolor="#FFFFCC"> 325<td> -auto</td> 326<td>boolean</td> 327<td>Turn off prompts</td> 328<td>Boolean value Yes/No</td> 329<td>N</td> 330</tr> 331 332<tr bgcolor="#FFFFCC"> 333<td> -stdout</td> 334<td>boolean</td> 335<td>Write first file to standard output</td> 336<td>Boolean value Yes/No</td> 337<td>N</td> 338</tr> 339 340<tr bgcolor="#FFFFCC"> 341<td> -filter</td> 342<td>boolean</td> 343<td>Read first file from standard input, write first file to standard output</td> 344<td>Boolean value Yes/No</td> 345<td>N</td> 346</tr> 347 348<tr bgcolor="#FFFFCC"> 349<td> -options</td> 350<td>boolean</td> 351<td>Prompt for standard and additional values</td> 352<td>Boolean value Yes/No</td> 353<td>N</td> 354</tr> 355 356<tr bgcolor="#FFFFCC"> 357<td> -debug</td> 358<td>boolean</td> 359<td>Write debug output to program.dbg</td> 360<td>Boolean value Yes/No</td> 361<td>N</td> 362</tr> 363 364<tr bgcolor="#FFFFCC"> 365<td> -verbose</td> 366<td>boolean</td> 367<td>Report some/full command line options</td> 368<td>Boolean value Yes/No</td> 369<td>Y</td> 370</tr> 371 372<tr bgcolor="#FFFFCC"> 373<td> -help</td> 374<td>boolean</td> 375<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td> 376<td>Boolean value Yes/No</td> 377<td>N</td> 378</tr> 379 380<tr bgcolor="#FFFFCC"> 381<td> -warning</td> 382<td>boolean</td> 383<td>Report warnings</td> 384<td>Boolean value Yes/No</td> 385<td>Y</td> 386</tr> 387 388<tr bgcolor="#FFFFCC"> 389<td> -error</td> 390<td>boolean</td> 391<td>Report errors</td> 392<td>Boolean value Yes/No</td> 393<td>Y</td> 394</tr> 395 396<tr bgcolor="#FFFFCC"> 397<td> -fatal</td> 398<td>boolean</td> 399<td>Report fatal errors</td> 400<td>Boolean value Yes/No</td> 401<td>Y</td> 402</tr> 403 404<tr bgcolor="#FFFFCC"> 405<td> -die</td> 406<td>boolean</td> 407<td>Report dying program messages</td> 408<td>Boolean value Yes/No</td> 409<td>Y</td> 410</tr> 411 412<tr bgcolor="#FFFFCC"> 413<td> -version</td> 414<td>boolean</td> 415<td>Report version number and exit</td> 416<td>Boolean value Yes/No</td> 417<td>N</td> 418</tr> 419 420</table> 421