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.