<CHAPTER ID="INTRODUCTION">
  <TITLE>Introduction to &prog;</TITLE>
  
  <SECT1 ID="WHATIS">
    <TITLE>What is &prog;?</TITLE>
    <PARA>
&prog; is a DNA sequence comparison viewer based on <ULINK
URL="http://www.sanger.ac.uk/Software/Artemis/"
type="external">Artemis</ULINK>.  The name &prog; stands for Artemis
Comparison Tool.  &prog; is written in Java, reads EMBL or GENBANK format
sequences and feature tables, and can work on sequences of any size.
    </PARA>

    <PARA>
The sequence comparison displayed by &prog; is usually the result of a blastn
or tblastx search that has been processed by <ULINK
URL="http://www.cgr.ki.se/cgr/groups/sonnhammer/MSPcrunch.html"
TYPE="external">MSPcrunch</ULINK>. MSPcrunch must be run with the -d flag for
the output to be usable by &prog;.  See <XREF LINKEND="COMPARISON-RUN"> for
more on MSPcrunch.
    </PARA>

    <PARA>
For more information go to <ULINK
URL="http://www.sanger.ac.uk/Software/Artemis/" TYPE="external">the &art;
web pages</ULINK> or the <ULINK
URL="http://www.sanger.ac.uk/Software/Artemis/ACT" TYPE="external">the &prog;
web pages</ULINK>.
    </PARA>
  </SECT1>

&requirements;

  <SECT1 ID="INSTALLATION">
    <TITLE>Getting and Installing &prog;</TITLE>
    <PARA>
The most up to date version of &prog; is always available from the <ULINK
URL="http://www.sanger.ac.uk/Software/Artemis/ACT">&prog; web pages</ULINK>.
    </PARA>

&gettingjava;

    <SECT2 ID="UNIXINSTALLATION">
      <TITLE>Installation Instructions for UNIX</TITLE>
      <PARA>
Change directory to the directory you wish to install &prog; in.  We will use
<LITERAL>~/</LITERAL> in this example and in the next chapter.  Uncompress and
untar the <LITERAL>act_compiled.tar.gz</LITERAL> file.  On UNIX the command
is:
      </PARA>
      <PARA>
         <COMMAND>
gzip -d &lt; act_compiled.tar.gz | tar xf -
         </COMMAND>
      </PARA>
      <PARA>
This will create a directory called <LITERAL>~/act</LITERAL> which will
contain all the files necessity for running &prog;.
      </PARA>
  
      <PARA>
For instructions on how to run &prog; on UNIX once it is unpacked see <XREF
LINKEND="RUNNINGUNIX">.
      </PARA>
    </SECT2>

    <SECT2 ID="MACINSTALLATION">
      <TITLE>Installation Instructions for Macintosh Systems</TITLE>
      <PARA>
Macintosh users should download and run the <LITERAL>ACT.bin</LITERAL> file
from the <ULINK URL="http://www.sanger.ac.uk/Software/Artemis/ACT">&prog; web
pages</ULINK>, which will create a local copy of the the &art; application
(along with an icon).
      </PARA>
    </SECT2>

    <SECT2 ID="DOSINSTALLATION">
      <TITLE>Installation Instructions for Windows</TITLE>
      <PARA>
On Windows systems with Java 1.2, installing &prog; is as simple as copying the
<ULINK URL="ftp://ftp.sanger.ac.uk/pub/pathogens/software/act/act.jar"
TYPE="external">act.jar file</ULINK> to an appropriate place (such as the
desktop or the Programs folder).
      </PARA>

      <PARA>
For instructions on how to run &prog; on Windows once it is unpacked see <XREF
LINKEND="RUNNINGPC"> .
      </PARA>
    </SECT2>
  </SECT1>

&concepts;

  <SECT1 ID="CONTRIBUTIONS">
    <TITLE>Contributions and Suggestions</TITLE> 
    <PARA> 
We welcome contributions to &prog; and to &art;, bug reports from users and
suggestions for new features.  An email discussion list has been set up for
this purpose.  To join, send a message to 'majordomo@sanger.ac.uk' with
'subscribe artemis' in the body (not the subject).  Announcements will
also be sent to this list. 
    </PARA>
  </SECT1>

&acknowledgements;

&copyright;

</CHAPTER>
