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)