--mb
MegaBLAST output filename
The input file should be a MegaBLAST output file, formatted with the -D 3 option.
Default value: none

--tiac
Output filename
This creates an output file with the filename given. If this filename does not already have a .tiac suffix, it will be automatically appended to it.
Default value: tiac

--db
Database name
The name of the database that was searched with MegaBLAST. This will be included in the description of the MegaBLAST search at the top of the tiac file, so that users can keep track of their parameters.
Default value: est

--evalue
Expectation value (double)
The expectation value used during the MegaBLAST search. As for --db, this will be included in the details at the top of the tiac file.
Default value: 1e-20

--error
Percentage sequence error (double)
Sets the maximum percentage sequence error permitted for a match to be considered.
Default value: 0.05 (i.e. 5% sequencing error tolerated)

--required-length
Minimum length (integer)
Sets the minimum HSP alignment length (between the query and the subject sequences) required for a match to be considered.
Default value: 150

--assemble-hsps

Accumulates the length of all HSPs from the same subject sequence and query sequence (which pass the sequence identity threshold).The total length of these HSPs is then used to determine if a match reaches the minimum length. This option is useful when processing output obtained from unspliced mRNA. In this case, exons in the query sequence often result in several HSPs individually shorter than the required alignment length. This option accumulates their length before applying the threshold.
Default value: false

--best-est

Instructs TImegablast to only associate an EST with a query sequence if that query sequence is the best match for that EST. It is advised that this option should be used in conjunction with --assemble-hsps.
Default value: false

--required-length
Minimum length (integer)
Minimum alignment length required to consider an hsp.
Default value: 150

--help

Print a help message.
Default value: false