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Typhon Manual |
| Option | Type | Default | Description |
| -startdb | unsigned int | The position at which to start indexing the database | |
| -enddb | unsigned int | The position at which to stop indexing the database | |
| -startq | unsigned int | The position at which to start scanning the query | |
| -endq | unsigned int | The position at which to stop scanning the query | |
| -mhl | unsigned int | If this is non-zero, hits longer than this will be broken into pieces no longer than this value | |
| -o | string | Write output to this file as oposed to stdout | |
| -outputlevel | [0,1,2] | 0 | Control the output level |
| -w | unsigned int | 10 | The weight of the pattern. Ignored if a pattern is specified |
| -s | unsigned int | 18 | The span of patterns |
| -pattern | {0,1}* | A pattern to run. This is used only if standard blast is run; it overrides word length | |
| -devs | float | 5 | Words occuring more frequently than this number of deviations above the mean are not indexed. |
| -S1 | unsigned int | Threshold (in bits) at which words are kept after the first round of ungapped extensions. Overrides E1 | |
| -S | unsigned int | Threshold (in bits) for HSPs (gapped or ungapped). Overrides E | |
| -gapS | unsigned int | Threshold (in bits) at which to do full gapped extensions on ungapped HSPs. Gapped HSPs must score higher than S to be kept as HSPs. Overrides gapE. | |
| -gap | Perform gapped extensions | ||
| -E1 | double | 10 | E value at which words are kept after the first round of ungapped extensions |
| -E | double | E1 | E valuefor HSPs (gapped or ungapped) |
| -gapE | double | E1 | E value at which to do full gapped extensions on ungapped HSPs. Gapped HSPs must score higher than S to be kept as HSPs |
| -X1 | unsigned int | 23 | When scores drop this far (in bits) below the best value seen so far, first round of ungapped extensions is stopped |
| -X2 | unsigned int | X1 | When scores drop this far (in bits) below the best value seen so far, final round of ungapped extensions is stopped |
| -gapX | unsigned int | 40 | When scores drop this far (in bits) below the best value seen so far, gapped extensions are stopped |
| -hitdist | unsigned int | 0 | If this is non-zero, then only pairs of hits within a window of this size on the same diagonal are extended |
| -matrix | filename | HOXD gapOpen=400 |
The scoring matrix to use |
| -nodust | Do not perform filtering using DUST on the query sequence | ||
| -dustl | unsigned int | 15 | Level at which to dust query |
| -P | unsigned int | 15 | Number of patterns to index. Used only is standard blast is not runa |
| -B | unsigned int | 2 | Number of patterns to index on average at each position. Used only is standard blast is not run |
| -sepq | Treat query file as a concatenation of multiple queries. Otherwise, it will be assumed to be a multiple alignment | ||
| -runblast | Run the basic blast algorithm | ||
| -runallpairs | Index not the consensus character but every letter in a sequence; valid only for runblast | ||
| -runpattern | Run the basic blast using a set of patterns; every position will be indexed equally | ||
| -queryname | string | The name of the query. It must match that in the tree exactly | |
| -numregionclasses | The number of region classes to use | ||
| -tree | filename | The phylogenetic tree. Entries must match the sequence names in the FASTA file exactly | |
| -patternfile | filename | A file consisting of the patterns to use. Only P will be used. Format is a list of patterns, one per line, each a bit string. Each will be formatted to have the input weight (w) and span (s) | |
| -memopt | Minimize memory usage; may degrade performance |
©2005 Jason Flannick and Serafim Batzoglou