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)