Installing Phylogena - the easy way
-----------------------------------

To install Phylogena on a Windows system, the easiest possibility 
is to unpack phylogenaEasy.zip under C:. (For manual installation, 
see Installing_Phylogena.pdf.)

A folder called phylogena will appear under C: with all the files 
required for Phylogena, in a working setup. The only costumization 
necessary is to specify the path to java.exe on your system in 
phylogena.bat (right click / edit). Replace the path in the following 
line with the path one your system:

set LOCAL_JAVA="C:\Program Files\Java\jre1.5.0_06\bin\java"

Java is normally installed under Program Files\Java in a folder wit
h a version name (like jre1.5.0_06). Java.exe can be found in the "bin" 
subfolder, i.e. most probably you only have to replace the version 
number in the above line (after \java and before \bin\java).

After this, you should be able to start phylogena by double clicking on 
phylogena.bat (a Windows command window will appear; do not close this 
as long as phylogena is running).

See Installing_phylogena.pdf for basic usage instructions. 

You can perform a test run with the fasta files provided in the sample 
folder under phylogena by importing them (File menu, import fasta sequences). 
The examples are protein sequences. After that, you can analyse them by 
clicking on Rules / Analyse whole project; you can accept defult settings 
for testing. The analysis should be finished in 30-60 seconds per sequence, 
depending on your system and the settings. After the analyses have completed 
(you will see "Analysis done" in the DOS command window), you can click on 
one of the sequence names and look at the multiple alignments (View / Show 
Alignment) and the trees (View / Show Tree).