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.