hyfi-distill

Description: Sorts a FASTA file lexicographically, and removes records. By default, only duplicate records are removed.

Usage: hyfi-distill [options] <FASTA file>

Input:

<FASTA file>: A space-delimited file of sequences and candidate binding partners. If a '-' is given instead of a filename, then standard input is read.

Output: A FASTA file with entries sorted lexicographically and possibly records removed.

Options:

• --dg-max <number>: pass all pairs that bind with at least the specified affinity, in units of kilocalories per mole. By default, this option is set so that all binding sites are reported.
• --dg-delta <number>: Pass all binding sites whose binding energy to the query is within the delta of the binding energy of the query to itself.
• --proximity <number>: only report records that are <number> bases upstream of another record in the set.
• -o <filename>: write output to the specified file, instead of the standard out.
• -v <number>: verbosity level. The verbosity is controlled by <number>; 0 means no extra output, and 5 means extreme verbosity. The default is 0.