Provided by: pilercr_1.06+dfsg-5_amd64
NAME
pilercr - software for finding CRISPR repeats
DESCRIPTION
pilercr v1.06 http://www.drive5.com/piler
AUTHOR
Written by Robert C. Edgar This software is donated to the public domain. Please visit web site for requested citation. Basic options: -in <filename> Sequence file to analyze (FASTA format). -out <filename> Report file name (plain text). -seq <filename> Save consensus sequences to this FASTA file. -trimseqs Eliminate similar seqs from -seq file. -noinfo Don't write help to report file. -quiet Don't write progress messages to stderr. Criteria for CRISPR detection, defaults in parentheses: -minarray <N> Must be at least <n> repeats in array (3). -mincons <F> Minimum conservation (0.9). At least N repeats must have identity >= F with the consensus sequence. Value is in range 0 .. 1.0. It is recommended to use a value < 1.0 because using 1.0 may suppress true arrays due to boundary misidentification. -minrepeat <L> Minimum repeat length (16). -maxrepeat <L> Maximum repeat length (64). -minspacer <L> Minimum spacer length (8). -maxspacer <L> Maximum spacer length (64). -minrepeatratio <R> Minimum repeat ratio (0.9). -minspacerratio <R> Minimum spacer ratio (0.75). 'Ratios' are defined as minlength / maxlength, thus a value close to 1.0 requires lengths to be similar, 1.0 means identical lengths. Spacer lengths sometimes vary significantly, so the default ratio is smaller. As with -mincons, using 1.0 is not recommended. Parameters for creating local alignments: -minhitlength <L> Minimum alignment length (16). -minid <F> Minimum identity (0.94).