NAME

       primeDLRS, primeGSRf - Guest-in-host tree reconciliation tool

SYNOPSIS

       primeDLRS [OPTIONS] seqfile hostfile [gsfile]

DESCRIPTION

       Guest-in-host  tree  reconciliation tool, enabling analysis of e.g. guest tree topologies,
       reconciliation properties and duplication-loss rates. Based on a Bayesian  MCMC  framework
       using  the  underlying GSR model. The old program name, primeGSRf, is still available as a
       symlink to primeDLRS.

       1)     the guest tree topology and its divergence times are modelled with  a  duplication-
              loss process in accordance with the Gene Evolution Model (GEM).

       2)     sequence evolution is modelled with a user-defined substitution model.

       3)     sequence  evolution  rate variation over guest tree edges (relaxed molecular clock)
              are modelled with iid values from a user-selected distribution.

       4)     sequence evolution rate variation over sites (positions) are modelled according  to
              a discretized Gamma distribution.

       The  implementation  uses  a  discretization of the host tree to perform its computations.
       Please review available options, as you will need to change default settings.   Option  -r
       may be useful to avoid numeric issues due to scaling.

       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|F81|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 sequence evolution  rate  variation  over  guest  tree  edges.
              Defaults to  (not to confuse with -Sn).

       -Ep FLOAT FLOAT
              Initial  mean  and variance of sequence evolution rate. Defaults to simple rule-of-
              thumb based on host tree times.

       -Ef    Fix mean and variance of sequence evolution rate. 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.

       -Gl    Fix  initial  guest  tree edge lengths (in addition to topology), i.e. fix the edge
              lengths. Non-fixed by default.

       -Bp FLOAT FLOAT
              Initial duplication and loss rates. Defaults to  and .

       -Bf    Fix initial duplication and loss rates. Non-fixed by default.

       -Bt FLOAT
              Override time span of edge above root in host tree. If the value is <=0,  the  span
              will  be  set  to equal the root-to-leaf time. Defaults to value in host tree file.
              See also option -Dtt.

       -Dt FLOAT
              Approximate discretization timestep. Set to 0 to divide every edge in equally  many
              parts (see -Di). Defaults to . See -Dtt for edge above root.

       -Di UNSIGNED_INT
              Minimum number of parts to slice each edge in. If -Dt is set to 0, this becomes the
              exact number of parts. Minimum 2. Defaults to . See -Dtt for edge above root.

       -Dtt UNSIGNED_INT
              Override number of discretization points for edge  above  root  in  host  tree.  By
              default,  irrespective  of  time  span,  this  is set to the number of points for a
              (hypothetical) root-to-leaf edge

       -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. Note that discretization
              parameters are NOT rescaled.

       -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

       primeDTLSR(1),   primeGEM(1),   showtree(1),   chainsaw(1),    reconcile(1),    reroot(1),
       tree2leafnames(1), treesize(1)