.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH DLESS "1" "May 2016" "dless 1.4" "User Commands"
.SH NAME
dless \- Attempts to identify elements under selection in all species or in
.SH 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.
.SH EXAMPLE
.SH OPTIONS
.HP
\fB\-\-rho\fR, \fB\-R\fR <rho>
.IP
(default 0.3)
.HP
\fB\-\-transitions\fR, \fB\-t\fR [~]<mu>,<nu>
.IP
Set the transition probabilities of the two\-state HMM using
the specified values of <mu> and <nu> (both between 0 and 1).
.HP
\fB\-\-phi\fR, \fB\-p\fR [~]<phi>
.IP
(default 0.5)
.HP
\fB\-\-target\-coverage\fR, \fB\-C\fR [~]<gamma>
.IP
(Alternative to transitions, use with \fB\-\-expected\-length\fR) 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 \fB\-\-expected\-length\fR, completely defines the
transition probabilities.
.HP
\fB\-\-expected\-length\fR, \fB\-E\fR [~]<omega>
.IP
(Alternative to \fB\-\-transitions\fR, use with \fB\-\-target\-coverage\fR) Set
transition probabilities such that the (prior) expected length
of a conserved element is <omega>.  The parameter mu is set to
1/omega.
.HP
\fB\-\-msa\-format\fR, \fB\-i\fR FASTA|PHYLIP|MPM|MAF|SS
.IP
Alignment format (default is to guess format from file contents).
Note that the program msa_view can be used for conversion.
.HP
\fB\-\-refseq\fR, \fB\-M\fR <fname>
.IP
(for use with \fB\-\-msa\-format\fR 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.
.HP
\fB\-\-refidx\fR, \fB\-r\fR <refseq_idx>
Use coordinate frame of specified sequence in output.
Default
.IP
value is 1, first sequence in alignment; 0 indicates
coordinate frame of entire multiple alignment.
.HP
\fB\-\-seqname\fR, \fB\-N\fR <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").
.HP
\fB\-\-idpref\fR, \fB\-P\fR <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").
.HP
\fB\-\-indel\-model\fR, \fB\-I\fR alpha,beta,tau[,alpha2,beta2,tau2]
.IP
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 \fB\-\-indel\-history\fR is not used, a
history will be inferred on the fly using a simple parsimony
algorithm.
.HP
\fB\-\-indel\-history\fR, \fB\-H\fR <file.ih>
.IP
(for use with \fB\-\-indel\-model\fR) Use the specified indel history (see
indelHistory).
.HP
\fB\-\-help\fR, \fB\-h\fR
.IP
Show this help message and exit.