Provided by: elph_1.0.1-2_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-pn : 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-moption: 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 (-mor-toptions)-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 forelphis maintained as a Texinfo manual. If theinfoandelphprograms are properly installed at your site, the commandinfoelphshould give you access to the complete manual.