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