.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH PHASTMOTIF "1" "May 2016" "phastMotif 1.4" "User Commands"
.SH NAME
phastMotif \- Predicts motifs from a set of multiple alignments.  Uses
.SH 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 \fB\-m\fR).  Various parameters
control the strategy for initialization (see below).
Currently, the F81 substitution model is assumed.
.SH USAGE
phastMotif [\-t <treefile>] [OPTIONS] <msa_list>
.SH OPTIONS
.HP
\fB\-t\fR <file> (Required unless \fB\-m\fR or \fB\-p\fR) Use specified tree topology for
all phylogenetic models (Newick format).
.TP
\fB\-i\fR <fmt>
Input format for alignment.  May be FASTA, PHYLIP, MPM, SS,
or MAF (default FASTA).
.HP
\fB\-b\fR <file> Read background model from specified file (.mod format).
.IP
By default, the background model is estimated
in a preprocessing step, by pooling all data.
.TP
\fB\-s\fR
Estimate a separate background model for each multiple alignment.
(Not yet implemented.)
.HP
\fB\-k\fR <size> Learn motifs of the specified size (default is 10).
.TP
\fB\-B\fR <n>
Report best <n> motifs (default 3).
.TP
\fB\-m\fR
MEME mode.  Use multinomial rather than phylogenetic
models.  Causes multiple alignments to be ignored \fB\-\-\fR any
gaps are discarded and all sequences are assumed
independent.
.HP
\fB\-d\fR <+lst> Use the discriminative training method of Segal et
al. (RECOMB'02), rather than EM.
The specified list
.IP
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 \fB\-m\fR.
\fB\-p\fR
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.
\fB\-n\fR <n>
Perform <n> random restarts and report the motif with highest
likelihood.  Default number is 10.  Ignored with \fB\-I\fR, \fB\-P\fR, and
\fB\-R\fR unless \fB\-S\fR is specified (see below).
.HP
\fB\-I\fR <mlst> Run the algorithm after a "soft" initialization with
.IP
each of the consensus sequences in the specified list.
At each position, <pc> pseudocounts (see \fB\-c\fR) 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.
\fB\-P\fR <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.
\fB\-R\fR <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.
\fB\-w\fR <n>
(for use with \fB\-I\fR, \fB\-P\fR, \fB\-R\fR) Winnow initialization sequences
to the top <n> based on the unmaximized likelihood.
.TP
\fB\-c\fR <pc>
(for use with \fB\-I\fR, \fB\-P\fR, \fB\-R\fR) Number of pseudocounts for
consensus bases (default 5).
\fB\-S\fR
(for use with \fB\-I\fR, \fB\-P\fR, \fB\-R\fR) Instead of doing a deterministic
initialization based on a consensus sequence, sample
parameters from a Dirichlet distribution defined by the
pseudocounts (see \fB\-c\fR).  In this case, random restarts
are performed, as specified by \fB\-n\fR.
.HP
\fB\-o\fR <pref> Use the specified prefix for all output files (dflt. "phastm").
\fB\-H\fR
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.
.TP
\fB\-D\fR
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.
.TP
\fB\-x\fR
(For use with \fB\-H\fR or \fB\-D\fR) Suppress ordinary output to stdout.
.TP
\fB\-h\fR
Print this help message.