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)