NAME

       phastOdds - Compute log-odds scores based on two phylogenetic models or phylo-HMMs,

DESCRIPTION

       Compute  log-odds  scores based on two phylogenetic models or phylo-HMMs, one for features
       of interest (e.g., coding exons, conserved regions) and one for background.   Will  either
       (1)  compute a score for each feature in an input set, and output the same set of features
       with scores; or (2) output a separate score for each position  in  fixed-step  WIG  format
       (http://genome.ucsc.edu/goldenPath/help/wiggle.html);  or  (3) compute scores in a sliding
       window of designated size, and output a three-column file, with the index of the center of
       each  window  followed by the score for that window on the positive strand, then the score
       for that window on the negative strand.  The default is to  assume  a  reference  sequence
       alignment, with the reference sequence appearing first; feature coordinates are assumed to
       be defined with respect to the reference sequence (see --refidx).

SYNOPSIS

       phastOdds [OPTIONS] --background-mods  <bmods>  [--background-hmm  <bhmm>]  --feature-mods
       <fmods> [--feature-hmm <fhmm>] ( --features <feats> | --window <size> ) <alignment>

       Arguments  <bmods>  and  <fmods> should be comma-delimited lists of phylogenetic models in
       .mod format (as produced by phyloFit), <feats> may be in GFF, BED, or genepred format, and
       <alignment>  may  be  in  FASTA format or an alternative format specified by --msa-format.
       HMM files should be in the format used by exoniphy.

EXAMPLE

       (See below for more details on options)

       1. Compute conservation scores for features in a GFF file, based on a

       model for conserved sites (conserved.mod) vs. a model of neutral evolution  (neutral.mod).
       (These models may be estimated with phyloFit or phastCons.)

              phastOdds  --background-mods  neutral.mod  --feature-mods  conserved.mod --features
              features.gff alignment.fa > scores.gff

       Features could alternatively be specified in  BED  or  genepred  format  (format  will  be
       auto-recognized).    The  program  can  be  made  to  produce  BED-formatted  output  with
       --output-bed.

       2. Compute conservation scores in a sliding window of size 100.

              phastOdds --background-mods neutral.mod --feature-mods conserved.mod  --window  100
              alignment.fa > scores.dat

       (Window  is  advanced one site at a time.  Window boundaries are defined in the coordinate
       frame of the multiple alignment, but center coordinates are converted to the frame of  the
       reference sequence as they are output.)

       3. Compute a "coding potential" score for features in a BED file, based on a phylo-HMM for
       coding regions versus a phylo-HMM  for  noncoding  DNA,  with  states  for  conserved  and
       nonconserved sequences.

              phastOdds   --background-mods   codon1.mod,codon2.mod,codon3.mod   --background-hmm
              coding.hmm   --feature-mods    neutral.mod,conserved-noncoding.mod    --feature-hmm
              noncoding.hmm --features features.bed --output-bed alignment.fa > scores.bed

OPTIONS

       --background-mods, -b <backgd_mods>

              (Required)  Comma-delimited  list  of  tree model (*.mod) files for background.  If
              used with --background-hmm, order of models must correspond to order of  states  in
              HMM.

       --background-hmm, -B <backgd.hmm>

       HMM for background.
              If there is only one backgound tree

              model, a trivial (single-state) HMM will be assumed.

       --feature-mods, -f <feat_mods> (Required) Comma-delimited list of tree model (*.mod) files
              for features.  If used with --feature-hmm, order of models must correspond to order
              of states in HMM.

       --feature-hmm,  -F  <feat.hmm>  HMM  for  features.   If  there is only one tree model for
              features, a trivial (single-state) HMM will be assumed.

       --features, -g <feats.gff>

              (Required unless -w or -y) File defining  features  to  be  scored  (GFF,  BED,  or
              genepred).

       --window,  -w  <size> (Can be used instead of -g or -y) Compute scores in a sliding window
              of the specified size.

       --base-by-base, -y

              (Can be used instead of -g or -y) Output base-by-base  scores,  in  the  coordinate
              frame of the reference sequence (or of the sequence specified by --refidx).  Output
              is in fixed-step WIG  format  (http://genome.ucsc.edu/goldenPath/help/wiggle.html).
              This  option can only be used with individual phylogenetic models, not with sets of
              models and a (nontrivial) HMM.

       --window-wig, -W <size>

              (Can be used instead of -g or -y) Like --window but outputs  scores  in  fixed-step
              WIG  format,  as  with  --base-by-base.   Scores  for  the positive strand only are
              output.

       --msa-format, -i <type>

       Input format for alignment.
              May be FASTA, PHYLIP, MPM, SS, or

              MAF (default is to guess format from file contents).

       --refidx, -r <ref_seq> Index of reference sequence for coordinates.  Use 0 to indicate the
              coordinate system of the alignment as a whole.  Default is 1, for first sequence.

       --output-bed, -d

              (For use with -g) Generate output in bed format rather than GFF.

       --verbose,  -v  Verbose  mode.   Print  messages  to stderr describing what the program is
              doing.

       --help, -h

              Print this help message.