PROGRAM: dmcondition

USAGE: dmcondition [OPTIONS] <MSA file> <mod file> <motif file> > out.dat

NOTE: One or both of the --cond-on-subs or cond-on-species options are
      required! See below for details...

DESCRIPTION: 

Produce a plain-text file describing states and positions in the emissions
matrix that need to be zeroed out in order to condition on site presence in
a given species and/or presence of substitutions in order to make a gain or
loss call. This can be supplied to dmsample within the alignments.lst file.
See dmsample -h for details.

EXAMPLES:

OPTIONS:
	
    --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.	

    --cond-on-species, -x <species name in alignment>
	Condition gain and loss calls in the hmm on presence of a site in a
	given species. This is useful if ChIP-based regions are used as inputs
	for motif finding. The effect is to prohibit motif loss predictions on
	branches leading to a species believed to contain a binding site based
	on ChIP (or other) evidence and prohibit gain predictions on branches
	leading away from that species.

    --cond-on-subs, -X
	Condition gain and loss predictions on presence of at least one
	substitution within a window believed to represent a binding site. This
	prevents gain/loss predictions on branches that contain no observable
	substitutions in the multiple alignment. The underlying algorithm uses
	Fitch parsimony to partition the tree into branches that do and do not
	contain substitutions for each motif window in the dataset and zeroes
	out the chain of gain and loss states in the emissions matrix 
	corresponding to combinations of branch and motif position that do not
	contain any substitutions to support such a prediction.

	If used in conjunction with --cond-on-species, states that are already
	zeroed out because they are incompatible with site presence in a
	given species will be skipped in this step.

    --nosubs, -n
	Toggle between modes for deciding whether to zero a branch given the
	character sets at parent and child node. The default mode is to zero
	branches if parent and child nodes have identical sets of characters,
	regardless of size. This option toggles the alternate mode, where
	branches are zeroed only if there are no scenarios that allow any
	possibility of substitution along a branch. That is, parent and child
	both have the same base sequence with only a single possibility at both
	nodes.
	
    --as-bed, -b <bedfile>
	Output the locations of individual zeroed states in a bed format.
	This expects the filename of the sequence file to be in the format
	"chrom.genomic-start.genomic-end.format" -- other formats will cause
	unpredictable behavior (read: segfaults).

    --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.

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