---
name: "phastMotif"
section: "1"
platform: "linux"
package: "phast"
version: "1.7+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/phastMotif"
---

# phastMotif(1)

Predicts motifs from a set of multiple alignments. Uses

## NAME

phastMotif - Predicts motifs from a set of multiple alignments.  Uses

## DESCRIPTION

Predicts motifs from a set of multiple alignments.  Uses an EM algorithm similar to that of MEME, but a motif is defined by phylogenetic models rather than multinomial distributions.  The specified multiple alignments may actually be single sequences (see **-m**).  Various parameters control the strategy for initialization (see below). Currently, the F81 substitution model is assumed.

## USAGE

phastMotif \[-t \<treefile\>\] \[OPTIONS\] \<msa\_list\>

## OPTIONS

**-t** \<file\> (Required unless **-m** or **-p**) Use specified tree topology for all phylogenetic models (Newick format).

- **-i** \<fmt\>

  Input format for alignment.  May be FASTA, PHYLIP, MPM, SS, or MAF (default FASTA).

**-b** \<file\> Read background model from specified file (.mod format).

-

  By default, the background model is estimated in a preprocessing step, by pooling all data.

- **-s**

  Estimate a separate background model for each multiple alignment. (Not yet implemented.)

**-k** \<size\> Learn motifs of the specified size (default is 10).

- **-B** \<n\>

  Report best \<n\> motifs (default 3).

- **-m**

  MEME mode.  Use multinomial rather than phylogenetic models.  Causes multiple alignments to be ignored **--** any gaps are discarded and all sequences are assumed independent.

**-d** \<+lst\> Use the discriminative training method of Segal et al. (RECOMB'02), rather than EM. The specified list

-

  should contain the filenames from msa\_list that are to be considered \*positive\* examples (containing the desired motif); all others will be considered negative examples.  Can be used with or without **-m**. **-p** Use "profile" models rather than phylogenetic models (characters in each alignment column assumed independent).  The resulting model is a hybrid of the full model and MEME's model.  Essentially, it uses the multiple alignments but not the phylogeny.  NOT YET IMPLEMENTED. **-n** \<n\> Perform \<n\> random restarts and report the motif with highest likelihood.  Default number is 10.  Ignored with **-I**, **-P**, and **-R** unless **-S** is specified (see below).

**-I** \<mlst\> Run the algorithm after a "soft" initialization with

-

  each of the consensus sequences in the specified list. At each position, \<pc\> pseudocounts (see **-c**) are given to the consensus base and 1 pseudocount to all other bases.  Each string must have length at most equal to the size of the motif.  If shorter, it is used as a "seed" for a motif, with flanking positions treated as wildcards. **-P** \<x,y\> Initialize with the x most prevalent y-tuples.  A soft initialization is performed, as above.  If y is less than the motif size, y-tuples are used as a "seed" for a motif, as above. **-R** \<x,y\> Initialize with a random sample of x y-tuples.  A soft initialization is performed, as above.  If y is less than the motif size, y-tuples are used as a "seed" for a motif, as above. **-w** \<n\> (for use with **-I**, **-P**, **-R**) Winnow initialization sequences to the top \<n\> based on the unmaximized likelihood.

- **-c** \<pc\>

  (for use with **-I**, **-P**, **-R**) Number of pseudocounts for consensus bases (default 5). **-S** (for use with **-I**, **-P**, **-R**) Instead of doing a deterministic initialization based on a consensus sequence, sample parameters from a Dirichlet distribution defined by the pseudocounts (see **-c**).  In this case, random restarts are performed, as specified by **-n**.

**-o** \<pref\> Use the specified prefix for all output files (dflt. "phastm"). **-H** Produce HTML formatted output, in addition to ordinary output. One file is produced per predicted motif, as well as a single HTML-formatted summary file.

- **-D**

  Produce a BED file with predicted motifs, for use in the UCSC browser.  Currently, sequence names must be formatted such as "chr10:102553847-102554897+", with the final '+' or '-' indicating strand.

- **-x**

  (For use with **-H** or **-D**) Suppress ordinary output to stdout.

- **-h**

  Print this help message.