primeDTLSR - Guest-in-host tree inference tool
primeDTLSR [OPTIONS] seqfile hostfile
[gsfile]
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.
- -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.
- 0
- Successful program execution.
- 1
- Some error occurred