NAME

       cgview_comparison_tool - visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences

DESCRIPTION

   USAGE:
              cgview_comparison_tool -p DIR [options]

   DESCRIPTION:
              Run  this  command  once  to  generate  a  project directory. After the project is created place a
              reference genome in the reference_genome directory and any genomes to compare with  the  reference
              in the comparison_genomes directory.

              [Optional] Make changes to the project_settings.conf file to configure how the maps will be drawn.
              Add additional GFF files to the features and analyis directories.

              Draw maps by running this command again with the '-p' option pointing to the project directory.

   REQUIRED ARGUMENTS:
       -p, --project DIR

              If no project exists yet, a blank project directory will be created.  If the project exists,  maps
              will be created.

       OPTIONAL ARGUMENTS:

       -s, --settings FILE

              The  settings  file.  If  none  is  provided,  the  default  settings  file  will  be  copied from
              $CCT_HOME/conf/project_settings.conf to the project directory.

       -g, --config FILE

              The configuration file. The default is to use the $CCT_HOME/conf/global_settings.conf file.

       -z, --map_size STRING

              Size of custom maps to create. For quickly generating new map sizes,  use  this  option  with  the
              --start_at_xml   option.  Possible  sizes  include  small/medium/large/x-large  or  a  combination
              separated by commas (e.g.  small,large). The size(s) provided will override  the  size(s)  in  the
              configuration files.

       -x, --start_at_xml

              Jump  to  XML  generation.  Skips  performing  blast,  which can speed map generation if blast has
              already been done. This option is for creating new maps after making changes to the  .conf  files.
              Note that any changes in the .conf files related to blast will be ignored.

       -r, --start_at_map

              Start  at  map  generation. Skips performing blast and generating XML. Useful if manual changes to
              the XML files have been made or if creating new map sizes (see --map_size).

       -f, --map_prefix STRING

              Prefix to be appended to map names (Default is to add no additional prefix).

       -b, --max_blast_comparisons INTEGER

              The maximum number of BLAST results sets to be passed to the XML creation phase (Default is 100).

       -t, --sort_blast_tracks

              Sort BLAST results such that genomes with highest similarity are plotted first.

       --cct

              Colour BLAST results based on percent identity of hit instead of  by  source  genome,  and  ignore
              'use_opacity' setting in configuration file.

       -m, --memory STRING

              Memory string to pass to Java's '-Xmx' option (Default is 1500m).

       -c, --custom STRINGS

              Settings used to customize the appearance of the map.

       -h, --help

              Show this message.

   EXAMPLE:
              cgview_comparison_tool -p my_project -b 50 -t \

       --custom tickLength=20 labelFontSize=15 --map_size medium,x-large

AUTHOR

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