.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.5.
.TH WARG "1" "December 2017" "warg 1.0" "User Commands"
.SH NAME
warg \- inference of homologous recombination in bacteria using whole genome sequences
.SH SYNOPSIS
.B warg
[OPTIONS] treefile datafile outputfile
.SH 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.
.SH OPTIONS
.TP
\fB\-w\fR NUM
Sets the number of pre burn\-in iterations (default is 100000)
.TP
\fB\-x\fR NUM
Sets the number of burn\-in iterations (default is 100000)
.TP
\fB\-y\fR NUM
Sets the number of iterations after burn\-in (default is 100000)
.TP
\fB\-z\fR NUM
Sets the number of iterations between samples (default is 100)
.TP
\fB\-T\fR NUM
Sets the value of theta. Use sNUM instead of NUM for per\-site
.TP
\fB\-R\fR NUM
Sets the value of rho. Use sNUM instead of NUM for per\-site
.TP
\fB\-D\fR NUM
Sets the value of delta
.TP
\fB\-s\fR NUM
Use given seed to initiate random number generator
.TP
\fB\-S\fR NUM,SEED
Run on a subset of NUM regions determined by seed SEED
.IP
NUM/NUM/../NUM
Run on a specified region(s) given by each NUM.
.TP
\fB\-r\fR NUM
Perform r tempered steps between topological updates (default:0)
.TP
\fB\-t\fR NUM
Tempered at "temperature" t for topological updates (default:1.0)
.TP
\fB\-U\fR
Start from UPGMA tree, rather than the default random tree.
.TP
\fB\-G\fR 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 \fB\-a\fR).  Note that this is NOT an MCMC move and causes bias.
.TP
\fB\-a\fR 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:
.IP
MoveRho (ignored if not needed)
.IP
MoveDelta (ignored if not needed)
.IP
MoveTheta (ignored if not needed)
.IP
MoveRemEdge
.IP
MoveAddEdge
.IP
MoveSiteChange
.IP
MoveTimeChange
.IP
MoveEdgeChange
.IP
MoveAgeClonal
.IP
MoveScaleTree
.IP
MoveRegraftClonal
.TP
\fB\-i\fR NUM,...,NUM
Set the SIX parameters for creating random Recombination Trees
under the inference model.  The parameters are:
.IP
N (integer)       The number of sequences in the sample (default 10)
.IP
n_B (integer)       The number of block boundaries in the sample (default 8)
.IP
l_B (integer)       The length of each block: L=n_B * l_B (default 500)
.IP
delta (real)          The average length of imports (default 500.0)
.IP
theta (real)          The mutation rate NOT per site (default 100.0)
.IP
rho (real)          The recombination rate NOT per site (default 50.0)
.TP
\fB\-f\fR
Forbid topology changes, (allowing updates of coalescence times).
.TP
\fB\-v\fR
Verbose mode
.TP
\fB\-h\fR
This help message
.TP
\fB\-V\fR
Print Version info
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.