NAME

       warg - inference of homologous recombination in bacteria using whole genome sequences

SYNOPSIS

       warg [OPTIONS] treefile datafile outputfile

DESCRIPTION

        Bacteria, unlike us, can reproduce on their own. They do however have
        mechanisms that transfer DNA between organisms, a process more formally
        known as recombination. The mechanisms by which recombination takes
        place have been studied extensively in the laboratory but much remains
        to be understood concerning how, when and where recombination takes
        place within natural populations of bacteria and how it helps them to
        adapt to new environments. ClonalOrigin performs a comparative analysis
        of the sequences of a sample of bacterial genomes in order to
        reconstruct the recombination events that have taken place in their
        ancestry.

OPTIONS

       -w NUM Sets the number of pre burn-in iterations (default is 100000)

       -x NUM Sets the number of burn-in iterations (default is 100000)

       -y NUM Sets the number of iterations after burn-in (default is 100000)

       -z NUM Sets the number of iterations between samples (default is 100)

       -T NUM Sets the value of theta. Use sNUM instead of NUM for per-site

       -R NUM Sets the value of rho. Use sNUM instead of NUM for per-site

       -D NUM Sets the value of delta

       -s NUM Use given seed to initiate random number generator

       -S NUM,SEED
              Run on a subset of NUM regions determined by seed SEED

              NUM/NUM/../NUM Run on a specified region(s) given by each NUM.

       -r NUM Perform r tempered steps between topological updates (default:0)

       -t NUM Tempered at "temperature" t for topological updates (default:1.0)

       -U     Start from UPGMA tree, rather than the default random tree.

       -G NUM Greedily  compute  the  "best  fit"  tree,  given the recombination observed on the
              current tree.  If NUM is negative and a previous  run  is  provided,  the  tree  is
              calculated  from  all  observed  values.   If  NUM  is positive, a "greedy move" is
              performed with weight NUM (see -a).  Note that this is NOT an MCMC move and  causes
              bias.

       -a NUM,...,NUM
              Set  the  ELEVEN (real valued) move weightings to the given vector, with weightings
              separated by commas (NOT SPACES).  The weightings need not sum to 1, but must be in
              the following order:

              MoveRho (ignored if not needed)

              MoveDelta (ignored if not needed)

              MoveTheta (ignored if not needed)

              MoveRemEdge

              MoveAddEdge

              MoveSiteChange

              MoveTimeChange

              MoveEdgeChange

              MoveAgeClonal

              MoveScaleTree

              MoveRegraftClonal

       -i NUM,...,NUM
              Set  the SIX parameters for creating random Recombination Trees under the inference
              model.  The parameters are:

              N (integer)       The number of sequences in the sample (default 10)

              n_B (integer)       The number of block boundaries in the sample (default 8)

              l_B (integer)       The length of each block: L=n_B * l_B (default 500)

              delta (real)          The average length of imports (default 500.0)

              theta (real)          The mutation rate NOT per site (default 100.0)

              rho (real)          The recombination rate NOT per site (default 50.0)

       -f     Forbid topology changes, (allowing updates of coalescence times).

       -v     Verbose mode

       -h     This help message

       -V     Print Version info

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.