Provided by: elph_1.0.1-4build1_amd64 
NAME
elph - ELPH
DESCRIPTION
Motif finder program ELPH (Estimated Locations of Pattern Hits) Usage:
elph <multi-fasta_file> [options] OR elph <multi-fasta_file-1> <multi-fasta_file-2> [-t <matrix>]
Options: -h : print this help -b : just brief results; don't print motif
-d : find significance deterministically -v : find motif deterministically
-o <out_file> : write output in <out_file> instead of stdout -m <motif> : use the given
pattern <motif> to compute its best fit matrix
to the data
-a : use aac residues; default = nucleotides residues
-s <seed>
: sets the seed for the random generation
-p n : n = no of iterations before deciding local maximum; plateau
period variable
-x : print maximum positions within sequences
-g : find significance of motif
-t <matrix>
: test if there is significant difference between the two
input files for a given motif matrix; <matrix> is the file containing the motif matrix
-l : compute Least Likely Consensus (LLC) for given motif
-r : in conjunction with -m option: motif is not necessarily in
the closest edit distance from input motif
-e : only when an additional file is used to test the significance
of the motif: find only the motifs that exactly match the input pattern (-m or -t options)
-n [0..5]
: degree of Markov chain used to generate the random file
used to test the significance of the motif default = 2
LEN=n : n = length of motif
ITERNO=n
: n = no of iterations to compute the global maximum;
default = 10
MAXLOOP=n
: n = no of iterations to compute the local maximum;
default = 500
SGFNO=n
: n = no of iterations to compute significance of motif;
default = 1000
SEE ALSO
The full documentation for elph is maintained as a Texinfo manual. If the info and elph programs are
properly installed at your site, the command
info elph
should give you access to the complete manual.
elph 1.0.1 March 2020 ELPH(1)