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