Provided by: elph_1.0.1-5_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.