run_gubbins - Online in the Cloud

PROGRAM:

NAME

run_gubbins - phylogenetic analysis of genome sequences

SYNOPSIS

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

DESCRIPTION

Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial
whole genome sequences.

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.

OPTIONS

positional arguments:
alignment_filename
Multifasta alignment file

optional arguments:
-h, --help
show this help message and exit

--outgroup OUTGROUP, -o OUTGROUP
Outgroup name for rerooting. A list of comma separated names can be used if they
form a clade

--starting_tree STARTING_TREE, -s STARTING_TREE
Starting tree

--use_time_stamp, -u
Use a time stamp in file names

--verbose, -v
Turn on debugging

--no_cleanup, -n
Don't cleanup intermediate files

--tree_builder TREE_BUILDER, -t TREE_BUILDER
Application to use for tree building [raxml|fasttree|hybrid], default RAxML

--iterations ITERATIONS, -i ITERATIONS
Maximum No. of iterations, default is 5

--min_snps MIN_SNPS, -m MIN_SNPS
Min SNPs to identify a recombination block, default is 3

--filter_percentage FILTER_PERCENTAGE, -f FILTER_PERCENTAGE
Filter out taxa with more than this percentage of gaps, default is 25

--prefix PREFIX, -p PREFIX
Add a prefix to the final output filenames

--threads THREADS, -c THREADS
Number of threads to run with RAXML, but only if a PTHREADS version is available

--converge_method CONVERGE_METHOD, -z CONVERGE_METHOD
Criteria to use to know when to halt iterations [weigh
ted_robinson_foulds|robinson_foulds|recombination]

--version
show program's version number and exit

--min_window_size MIN_WINDOW_SIZE, -a MIN_WINDOW_SIZE
Minimum window size, default 100

--max_window_size MAX_WINDOW_SIZE, -b MAX_WINDOW_SIZE
Maximum window size, default 10000

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