How do I get slcview?

slcview is freely available under the GNU General Public License.

You can download it at http://prdownloads.sourceforge.net/slcview/slcview-1.1.2.tar.gz?download.

What do I need to run slcview?

slcview requires the following:

• Perl. I use 5.6.1 for i386-linux. It may work for earlier versions but I haven't tested it. Although I do know for a fact that there are some slight code modifications needed to run under 5.0005_03, which is what SourceForge's web servers are running. (If you really want to do this, comment out the line &Getopt::Long::Configure qw(pass_through);)
  
• The Perl interface for ImageMagick. I use version 5.4.1. I know for a fact that the program requires modification if you are using a version earlier than 4.2.8, because I had to change a few things to make the dynamic pictures at the top of the page work right on SourceForge's web server, which runs ImageMagick 4.2.8.
  
• Ghostscript. I use version 6.53. This is required by ImageMagick to write text onto images. SourceForge's web server doesn't seem to have this available to cgi scripts, so that's why the scale bar at the top of the page doesn't have any labels on it. If you don't care for text labels, and will annotate your scale bars yourself, then this is not really necessary. (As you can see above, drawing all the clustergrams and tree diagrams works fine without it.)

I run it on an x86 machine running Debian Linux. If you have Perl 5.6.1, ImageMagick 5.4.1 with the perl libraries installed, and Ghostscript 6.53, you should be all set. I haven't tested it under any other environments, but Perl, ImageMagick, and Ghostscript are supposed to be available on a wide variety of platforms...but I'm not going to be able to help you much if your configuration differs a lot from mine. If you're not sure whether you have everything you need, here are a few hints:

• At a command prompt, run
  system-prompt$ perl --version
  This will tell you what version of Perl you have. Look for 5.6.1 or later.
  
  
• If you have the right version of Perl, try this next:
  system-prompt$ perl -e 'use Image::Magick;'
  If you don't have the Image::Magick libraries for Perl installed, it should give you an error. If you do have them installed, it shouldn't do anything.

If you run slcview.pl by itself without any command line options, it will display a help file which tells you the syntax and all the options it knows about.

The real quick guide to using slcview is to run the following:
system-prompt$ ./slcview.pl foo.cdt -o foo.gif
(This assumes that slcview.pl and your foo.cdt file are in the same directory.)
This will read in the foo.cdt file, and look for a foo.gtr and foo.atr file. If it finds either of those, it will draw the gene tree or array tree diagrams as well. The output all goes into the foo.gif file.

If you have any comments or questions please let me know - if you just find it a little useful, or if you have suggestions about features or the code and it's organization.
You can email me at slchen@users.sourceforge.net.

I want to improve/add features to slcview!

slcview is open source under the GNU General Public License. So if you want to hack around with the source, go ahead! The project homepage on SourceForge.net is at http://sourceforge.net/projects/slcview. If you have a SourceForge account and would like to help with some feature additions or bug fixes, just let me know. And thanks!