---
name: "elph"
section: "1"
platform: "linux"
package: "elph"
version: "1.0.1-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/elph"
---

# elph(1)

ELPH

## 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

- **-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

## SEE ALSO

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.