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

SEE ALSO

       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.

AUTHOR

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