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

       elph - ELPH

       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

              infoelph

       should give you access to the complete manual.

elph 1.0.1                                          June 2020                                            ELPH(1)