Provided by: elph_1.0.1-2_amd64
elph - ELPH
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
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.