.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH RUN_GUBBINS "1" "Julu 2016" "run_gubbins 2.0.0" "User Commands"
.SH NAME
run_gubbins \- phylogenetic analysis of genome sequences
.SH SYNOPSIS
.B run_gubbins
[\-h] [\-\-outgroup OUTGROUP] [\-\-starting_tree STARTING_TREE]
[\-\-use_time_stamp] [\-\-verbose] [\-\-no_cleanup]
[\-\-tree_builder TREE_BUILDER] [\-\-iterations ITERATIONS]
[\-\-min_snps MIN_SNPS]
[\-\-filter_percentage FILTER_PERCENTAGE] [\-\-prefix PREFIX]
[\-\-threads THREADS] [\-\-converge_method CONVERGE_METHOD]
[\-\-version] [\-\-min_window_size MIN_WINDOW_SIZE]
[\-\-max_window_size MAX_WINDOW_SIZE]
alignment_filename
.SH DESCRIPTION
Gubbins supports rapid phylogenetic analysis of large samples of
recombinant bacterial whole genome sequences.
.P
Gubbins (Genealogies Unbiased By recomBinations In Nucleotide
Sequences) is an algorithm that iteratively identifies loci containing
elevated densities of base substitutions while concurrently constructing
a phylogeny based on the putative point mutations outside of these
regions. Simulations demonstrate the algorithm generates highly accurate
reconstructions under realistic models of short-term bacterial
evolution, and can be run in only a few hours on alignments of hundreds
of bacterial genome sequences.
.SH OPTIONS
.SS "positional arguments:"
.TP
alignment_filename
Multifasta alignment file
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-outgroup\fR OUTGROUP, \fB\-o\fR OUTGROUP
Outgroup name for rerooting. A list of comma separated
names can be used if they form a clade
.TP
\fB\-\-starting_tree\fR STARTING_TREE, \fB\-s\fR STARTING_TREE
Starting tree
.TP
\fB\-\-use_time_stamp\fR, \fB\-u\fR
Use a time stamp in file names
.TP
\fB\-\-verbose\fR, \fB\-v\fR
Turn on debugging
.TP
\fB\-\-no_cleanup\fR, \fB\-n\fR
Don't cleanup intermediate files
.TP
\fB\-\-tree_builder\fR TREE_BUILDER, \fB\-t\fR TREE_BUILDER
Application to use for tree building
[raxml|fasttree|hybrid], default RAxML
.TP
\fB\-\-iterations\fR ITERATIONS, \fB\-i\fR ITERATIONS
Maximum No. of iterations, default is 5
.TP
\fB\-\-min_snps\fR MIN_SNPS, \fB\-m\fR MIN_SNPS
Min SNPs to identify a recombination block, default is
3
.TP
\fB\-\-filter_percentage\fR FILTER_PERCENTAGE, \fB\-f\fR FILTER_PERCENTAGE
Filter out taxa with more than this percentage of
gaps, default is 25
.TP
\fB\-\-prefix\fR PREFIX, \fB\-p\fR PREFIX
Add a prefix to the final output filenames
.TP
\fB\-\-threads\fR THREADS, \fB\-c\fR THREADS
Number of threads to run with RAXML, but only if a
PTHREADS version is available
.TP
\fB\-\-converge_method\fR CONVERGE_METHOD, \fB\-z\fR CONVERGE_METHOD
Criteria to use to know when to halt iterations [weigh
ted_robinson_foulds|robinson_foulds|recombination]
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-\-min_window_size\fR MIN_WINDOW_SIZE, \fB\-a\fR MIN_WINDOW_SIZE
Minimum window size, default 100
.TP
\fB\-\-max_window_size\fR MAX_WINDOW_SIZE, \fB\-b\fR MAX_WINDOW_SIZE
Maximum window size, default 10000
.SH SEE ALSO
.PP
Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley
S. D., Parkhill J., Harris S.R. "Rapid phylogenetic analysis of large samples
of recombinant bacterial whole genome sequences using Gubbins". Nucleic Acids
Res. 2015 Feb 18;43(3):e15. doi: 10.1093/nar/gku1196.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can
be used for any other usage of the program.