NAME¶
primeDTLSR - Guest-in-host tree inference tool
SYNOPSIS¶
primeDTLSR [
OPTIONS]
seqfile hostfile [gsfile]
DESCRIPTION¶
Guest-in-host tree inference enabling reconciliation analysis using the
underlying DTLRS model. Model properties:
- 1)
- The guest tree topology evolves inside the host tree by means of
duplication, loss and horizontal transfer events guided by homogeneous
rates, much like a birth-death process. Lineages branch deterministically
at host tree nodes.
- 2)
- Relaxed molecular clock; sequence evolution rate variation over guest tree
edges. Rates are drawn iid from specified distribution. Also, rate
variation over sites may be added, using discretized gamma distribution
with mean 1.
- 3)
- Substitution model of choice; standard or user-defined. The implementation
uses a discretization of the host tree to approximate the probability of
all possible reconciliation realizations for the current parameter
state.
The implementation uses a discretization of the host tree to approximate the
probability of all possible reconciliation realizations for the current
parameter state.
seqfile is a file with aligned sequences for guest tree leaves.
hostfile is a PrIME Newick file with host tree incl. divergence times.
Leaves must have time 0 and root have time > 0.
gsfile is a tab-delimited file relating guest tree leaves to host tree
leaves if info not included in
hostfile.
OPTIONS¶
- -h, -u, -?
- Display help (this text).
- -o FILE
- Output filename. Defaults to stderr.
- -s UNSIGNED_INT
- Seed for pseudo-random number generator. Defaults to random seed.
- -i UNSIGNED_INT
- Number of iterations. Defaults to .
- -t UNSIGNED_INT
- Thinning, i.e. sample every <value>-th iteration. Defaults to .
- -w UNSIGNED_INT
- Output diagnostics to stderr every <value>-th sample. Defaults to
.
- -q
- Do not output diagnostics. Non-quiet by default.
- -m MCMC|PDHC|PD
- Execution type (MCMC, posterior density hill-climbing from initial values,
or just initial posterior density). Defaults to .
- -Sm UniformAA|JC69|JTT|UniformCodon|ArveCodon
- Substitution model. by default.
- -Su DNA|AminoAcid|Codon <Pi=float1 float2 ... floatn>
<R=float1 float2 ...float(n*(n-1)/2)>
- User-defined substitution model. The size of Pi and R must fit data type
(DNA: n=4, AminoAcid: n=20, Codon: n=62). R is given as a flattened upper
triangular matrix. Don't use both option -Su and -Sm.
- -Sn UNSIGNED_INT
- Number of steps of discretized Gamma-distribution for sequence evolution
rate variation over sites. Defaults to (no variation).
- -Ed Gamma|InvG|LogN|Uniform
- Distribution for IID rate variation among edges. Defaults to .
- -Ep FLOAT FLOAT
-
Initial mean and variance of edge rate distribution. Defaults to and .
- -Ef
- Fix mean and variance of edge rate distribution. Non-fixed by
default.
- -Gi FILE
- Filename with initial guest tree topology.
- -Gg
- Fix initial guest tree topology, i.e. perform no branch-swapping.
Non-fixed by default.
- -Bp FLOAT FLOAT
FLOAT
- Initial duplication, loss and transfer rates. Defaults to , and .
- -Bf
- Fix duplication, loss and transfer rates to initial values. Non-fixed by
default.
- -Bt FLOAT
- Override time span of edge above root in host tree. Must be greater than
0. Defaults to file-contained value.
- -Dt FLOAT
- Approximate discretization timestep. Set to 0 to divide edge generations
into the same amount of parts (see -Di). Defaults to .
- -Di UNSIGNED_INT
- Minimum number of discretization subintervals per edge generation. If -Dt
is set 0, this becomes the exact number of subintervals. Minimum 2.
@Defaults to conf_value_from_cmake_DiscMinIvs@.
- -C UNSIGNED_INT
- Number of transfer counts during sampling. Defaults to .
- -r
- Rescale the host tree so that the root-to-leaf time equals 1.0. All
inferred parameters will refer to the new scale. Off by default.
- -Z
- Do not print elapsed wall time and CPU time
- -W
- Do not print the command line
- -debuginfo
- Show misc. info to stderr before iterating. Not shown by default.
EXIT STATUS¶
- 0
- Successful program execution.
- 1
- Some error occurred
URL¶
- The prime-phylo home page: http://prime.sbc.su.se
-
SEE ALSO¶
primeDLRS(1),
primeGEM(1),
showtree(1),
chainsaw(1),
reconcile(1),
reroot(1),
tree2leafnames(1),
treesize(1)