Typhon Manual

Back

Command quick reference

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

Back