## table of contents

WARG(1) | User Commands | WARG(1) |

# 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)

# AUTHOR¶

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

December 2017 | warg 1.0 |