Provided by: elph_1.0.1-2_amd64 bug


       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

              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

       -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

       -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

              : n = no of iterations to compute the global maximum;

              default = 10

              : n = no of iterations to compute the local maximum;

              default = 500

              : 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.