PROGRAM: dmotif (Detection of Lineage Specific Motifs)

USAGE: dmotif [OPTIONS] alignment neutral.mod motif.pfm > out.gff

DESCRIPTION: 

TBD

EXAMPLES:

OPTIONS:

    --rho, -R <rho>
        (default 0.3)

    --phi, -p [~]<phi>
        (default 0.5)

    --zeta, -z [~]<zeta>
        Motif entry parameter for conserved sequences (default 0.001)

    --xi, -x [~]<xi>
	Motif entry parameter for nonconserved sequences (default 0.001)

    --xi-off, -F	
	Use the alternate model parameterization (single motif entry
	parameter) instead of the default (separate motif entry parameters
	for nonconserved (xi) and conserved sequences (zeta)).
	
    --target-coverage, -C [~]<gamma>
        (Alternative to transitions, use with --expected-length) Set
        the transition parameters such that the expected fraction of
        sites in conserved elements is <gamma> (betwen 0 and 1).  This
        is a *prior* rather than *posterior* expectation and assumes
        stationarity of the state-transition process.  This option
        causes the ratio mu/nu to be fixed at (1-gamma)/gamma, and
        together with --expected-length, completely defines the
        transition probabilities.

    --expected-length, -E [~]<omega>
        (Alternative to --transitions, use with --target-coverage) Set
        transition probabilities such that the (prior) expected length
        of a conserved element is <omega>.  The parameter mu is set to
        1/omega.

    --transitions, -t [~]<mu>,<nu> 
        Set the transition probabilities of the two-state HMM using
        the specified values of <mu> and <nu> (both between 0 and 1).

    --mot-mod-type, -S F81|HB
	Set the substitution model type used for motif states. Default is HB.
	With HB, the Halpern-Bruno model (1998. MBE. 15(7):910-917) will be
	used on motif branches, with site-specific selective pressure modeled
	through the rate matrix and equilibrium frequencies; branch lengths are
	not scaled by rho on motif branches. With F81, motif branches are
	explicitly scaled by rho and only equilibrium frequencies will be used
	in the substitution model for these branches. All branches are scaled 
	equally, by rho, regardless of constraint implied by the motif weight
	matrix, which implies equal constraint at all motif positions.

    --scale-by-branch, -B
	Scale transition probabilities for lineage-specific states by the
	branch length leading to the node predicted to contain the gain or
	loss event. Default is to treat all branches as if they were of equal
	length when assigning transition probabilities.

    --xi-off, -M
	Toggle between default and alternate parameterization for entry into
	motif states. Default parameterization uses zeta for transitions into
	conserved and lineage-specific motifs and xi for entry into 
	nonconserved motif states. Alternate parameterization uses a single
	zeta parameter for both types of transitions.

    --msa-format, -i FASTA|PHYLIP|MPM|MAF|SS
        Alignment format (default FASTA).  Note that the program
        msa_view can be used for conversion.

    --refseq, -M <fname>
        (for use with --msa-format MAF) Read the complete text of the
        reference sequence from <fname> (FASTA format) and combine it
        with the contents of the MAF file to produce a complete,
        ordered representation of the alignment.  The reference
        sequence of the MAF file is assumed to be the one that appears
        first in each block.

    --refidx, -r <refseq_idx>
        Use coordinate frame of specified sequence in output.  Default
        value is 1, first sequence in alignment; 0 indicates
        coordinate frame of entire multiple alignment.

    --seqname, -N <name>
        Use specified string for 'seqname' (GFF) or 'chrom' field in
        output file.  Default is obtained from input file name (double
        filename root, e.g., "chr22" if input file is "chr22.35.ss").

    --idpref, -P <name>
        Use specified string as prefix of generated ids in output
        file.  Can be used to ensure ids are unique.  Default is
        obtained from input file name (single filename root, e.g.,
        "chr22.35" if input file is "chr22.35.ss").

    --indel-model, -I alpha,beta,tau[,alpha2,beta2,tau2]
        Use a simple model of insertions and deletions that assumes a known
        indel history and at most one indel per branch of the tree at any
        given position.  The parameters alpha and beta are rates of
        insertion and deletion, respectively, per expected substitution per
        site, and the parameter tau is approximately the inverse of the
        expected indel length (see indelFit).  If two sets are parameters
        are given the first will be used for nonconserved regions and the
        second for conserved regions.  If --indel-history is not used, a
        history will be inferred on the fly using a simple parsimony
        algorithm.

    --indel-history, -H <file.ih>
        (for use with --indel-model) Use the specified indel history (see
        indelHistory).

    --score-list
        Print a complete list of log-odds scores for all motif states. This
        is useful for generating a null distribution of motif scores based
        on a neutral dataset. Only emission probabilities are used for these
        score and nothing will be estimated. Indel model and missing data
        are not considered, and scores will not reflect adjustments for
        either case.

    --help, -h
        Show this help message and exit.