.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH ELPH "1" "June 2020" "elph 1.0.1" "User Commands"
.SH NAME
elph \- ELPH
.SH DESCRIPTION
Motif finder program ELPH (Estimated Locations of Pattern Hits)
Usage:
.IP
elph <multi\-fasta_file> [options] OR
elph <multi\-fasta_file\-1> <multi\-fasta_file\-2> [\-t <matrix>]
Options:
\fB\-h\fR             : print this help
\fB\-b\fR             : just brief results; don't print motif
\fB\-d\fR             : find significance deterministically
\fB\-v\fR             : find motif deterministically
\fB\-o\fR <out_file>  : write output in <out_file> instead of stdout
\fB\-m\fR <motif>     : use the given pattern <motif> to compute its best fit matrix
.IP
to the data
.TP
\fB\-a\fR
: use aac residues; default = nucleotides residues
.TP
\fB\-s\fR <seed>
: sets the seed for the random generation
.TP
\fB\-p\fR n
: n = no of iterations before deciding local maximum; plateau
.IP
period variable
.TP
\fB\-x\fR
: print maximum positions within sequences
.TP
\fB\-g\fR
: find significance of motif
.TP
\fB\-t\fR <matrix>
: test if there is significant difference between the two
.IP
input files for a given motif matrix; <matrix> is the file
containing the motif matrix
.TP
\fB\-l\fR
: compute Least Likely Consensus (LLC) for given motif
.TP
\fB\-r\fR
: in conjunction with \fB\-m\fR option: motif is not necessarily in
.IP
the closest edit distance from input motif
.TP
\fB\-e\fR
: only when an additional file is used to test the significance
.IP
of the motif: find only the motifs that exactly match the
input pattern (\fB\-m\fR or \fB\-t\fR options)
.TP
\fB\-n\fR [0..5]
: degree of Markov chain used to generate the random file
.IP
used to test the significance of the motif
default = 2
.TP
LEN=n
: n = length of motif
.TP
ITERNO=n
: n = no of iterations to compute the global maximum;
.IP
default = 10
.TP
MAXLOOP=n
: n = no of iterations to compute the local maximum;
.IP
default = 500
.TP
SGFNO=n
: n = no of iterations to compute significance of motif;
.IP
default = 1000
.SH "SEE ALSO"
The full documentation for
.B elph
is maintained as a Texinfo manual.  If the
.B info
and
.B elph
programs are properly installed at your site, the command
.IP
.B info elph
.PP
should give you access to the complete manual.