SYNOPSIS
primeDTLSR [OPTIONS] seqfile hostfile [gsfile]DESCRIPTION
Guestinhost 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 birthdeath 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 userdefined. 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 tabdelimited 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 pseudorandom 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. Nonquiet by default.
 m MCMCPDHCPD
 Execution type (MCMC, posterior density hillclimbing from initial values, or just initial posterior density). Defaults to .
 Sm UniformAAJC69JTTUniformCodonArveCodon
 Substitution model. by default.
 Su DNAAminoAcidCodon <Pi=float1 float2 ... floatn> <R=float1 float2 ...float(n*(n1)/2)>
 Userdefined 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 Gammadistribution for sequence evolution rate variation over sites. Defaults to (no variation).
 Ed GammaInvGLogNUniform
 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. Nonfixed by default.
 Gi FILE
 Filename with initial guest tree topology.
 Gg
 Fix initial guest tree topology, i.e. perform no branchswapping. Nonfixed 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. Nonfixed by default.
 Bt FLOAT
 Override time span of edge above root in host tree. Must be greater than 0. Defaults to filecontained 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 [email protected]
 C UNSIGNED_INT
 Number of transfer counts during sampling. Defaults to .
 r
 Rescale the host tree so that the roottoleaf 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 primephylo home page: http://prime.sbc.su.se
