NAME

       dless - Attempts to identify elements under selection in all species or in

DESCRIPTION

       Attempts to identify elements under selection in all species or in some subset of species,
       based on a multiple alignment and a phylo-HMM.  In particular, detects elements that  have
       been  under  selection  since  the  divergence  of all species in the given set, that were
       "born" on some branch of the tree since their divergence and  have  been  under  selection
       since,  or  that  were  present  in  the  common  ancestor  but "died" (ceased to be under
       selection) on some branch of the tree.  Currently only  detects  negative  selection,  but
       extensions to detect positive selection as well are planned.

EXAMPLE

OPTIONS

       --rho, -R <rho>

              (default 0.3)

       --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).

       --phi, -p [~]<phi>

              (default 0.5)

       --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.

       --msa-format, -i FASTA|PHYLIP|MPM|MAF|SS

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

       --help, -h

              Show this help message and exit.