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.