pfsearchV3 - search protein and DNA generalized profiles (version 3)

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

pfsearchV3 3                                       March 2017                                      PFSEARCHV3(1)

       Build  protein  and  DNA  generalized  profiles  and  use  them  to  scan and align sequences, and search
       databases.

       pfsearchV3 - search protein and DNA generalized profiles (version 3)

Profile--level
              [-l] : level to use for cutoff

       --mode [-m] : mode to use for normalization

   Database--create-index-database
              [-c] : output indices to given file

       --use-index-database
              [-i] : use indices stored in given file

   Heuristic--cutoff
              [-C] : heuristic cutoff value

       --dump-heuristic-scores
              [-A] : only print heuristic scores to stdout

       --dump-heuristic-sequences [-D] : dump passed heuristic sequences

   Filter--dump-filter-scores
              [-a] : only print filter scores to stdout

       --dump-filter-sequences
              [-d] : dump passed heuristic and filter sequences

   Optimizations--sse2 [-s] : enforces SSE 2 only instruction set

       --nthreads
              [-t] : max number of threads to use

       --max-heuristic-nthreads
              [-T] : max number of threads to use for heuristic phase only. (IO bounds)

       --no-affinity
              [-f] : disable CPU affinity file

       --thread-affinity
              [-M] : file containing thread mask, one row for one thread

       --no-shared-core
              [-k] : Prevent core resource sharing

       --split
              [-b] : if both SSE 2 & 4.1 are available, split half-half using linked resources

   Printingoutput--output-method
              [-o] : printing output method

              == 0 replicates the pfseach output without options (DEFAULT)

              == 1 simple output

              == 2 replicates pfsearch -lxz output

              == 3 replicates pfscan -lxz output

              == 4 tsv output (single line tab delimited)

       --output-length
              [-W] : maximum number of column for sequence output printing

   Other--verbose
              [-v] : verbose on stderr

       --help [-h] : output command help

pfsearch [options] profile database