This is the command primeDTLSR that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use primeDTLSR online using onworks.net services
