PhyloGen v1.0, 2002 Andrew Rambaut 
Department of Zoology, University of Oxford, Oxford, UK 
Website: <http://evolve.zoo.ox.ac.uk> 
Email: andrew.rambaut@zoo.ox.ac.uk 
Please report any bugs or suggestions to the author. 

This document describes the UNIX version of PhyloGen v1.0

This program should compile with the latest version of gcc on most UNIX and Linux 
type systems. I may work with other C++ compilers. To do this you will have to edit
the Makefile (to change the name of the compiler from 'gcc' to 'CC' or whatever it may
be).

Note: there are a lot of files in the source because this uses my entire C++ class library. 
A lot of this code is not used (and will automatically stripped out of the program) but 
is required when compiling. I may be able to improve this situation later.

To compile type:

"make"

I suggest you then type

"make clean"

to get rid the temporary files.

This will leave you with an executable called 'phylogen'.

Type 

"./phylogen"

to run it or move it into your bin directory.

Running PhyloGen gives you a prompt at which you can type commands.
Type "help" to get a list of commands and "help <command>" to get help about a
command called <command>. The HTML document "help.html" has a complete 
list of all the commands.

The HTML document "manual.html" contains more details about the actual commands
and how to run the program.

