VELMA Files

Everything needed to run velma should be contained in this archive (including several test files and alignments).  Further work will wrap the velma jar files, the velma dependencies, and supporting data files in a clickable executable (or as a java web start).

For now, I have prepared two scripts (one for windows, one for unix-alikes) that can be run from the shell prompt.

1.) Extract the velma archive to some accessible location
2.) Run cmd.exe (or a terminal on osx/linux) and "cd" to the directory where extracted the velma folder.
3.) (windows) type: velma.bat at the prompt
    (osx/linux) type: ./velma.sh 

You should see a blue screen with a single active menu entitled "File". Click and select "Open alignment file".

The default working directory is the current directory (which should be the one where you unzipped the velma directoy).  You can select one of the test alignments, or browse the fielsystem to find an amino acid (no nucleotide, yet) alignment in any of the common alignment formats.

I am working on putting together a manual and video to illustrate the functionality of velma.  Once I have a woring draft of these materials I will post them to the sourceforge site.