Biosys2 refactorization/recompliation
Mark A. Jensen/Fortinbras Research
jensen@fortinbras.us
31 Jan 2009
mod 5 Feb 2009

This distribution contains FORTRAN source code for BIOSYS2, an early
version of what grew up to be PAUP*.

The original source by William C. Black was obtained from a directory at
lamar.colostate.edu, ftp://lamar.colostate.edu/pub/wcb4/. I was able
to obtain the zipped versions of the original source by issuing the
following ftp commands:

ftp> open ftp://anonymous@lamar.colostate.edu
ftp> cd pub
ftp> cd wcb4
ftp> mget *

The source has been modified to compile on Win32 (Vista/2000/NT) under
GNU Fortran as implemented in Cygwin. Some bugs and other issues have
been fixed along the way. The dimensions of the arrays for alleles,
etc., have been bumped up to 200 elements each. This should 
give some scope to 21st century computers. It is truly easy to modify
this if more space is needed; contact me via email for details. 

The distribution contains an executable, biosys2.exe, that is suitable
for running on the Windows command line. No compiler or funky shell is
required.

RUNNING GNU FORTRAN BIOSYS2

The cygwin1.dll accompanies this distribution. If you do not already
run Cygwin, then place this file in your PATH, or biosys2.exe will crash.
The utility dos2unix.exe also requires this .dll.

Two principles are key to running the .exe in this 
distribution:

1: Currently, The input files MUST have UNIX (not DOS)
   linebreaks. This means all lines end with ASCII 10 (CR) only, not
   ASCII 10, ASCII 13 (CR/LF). Conversion programs are available in
   abundance; search for 'linebreak', 'DOS to UNIX format', 'UNIX text
   files', etc.

   The Cygwin utility dos2exe accompanies this distribution. To 
   convert a DOS datafile to Unix format, simply do

   c:> dos2unix.exe -U datafile.bio

2: The code has been rewritten to read a datafile from standard input
   (stdin), and send the analysis to standard output (stdout). To make
   this work at the DOS command line, you need to use the 'redirection
   symbols' < and >. Run this example from the distribution directory:

   C:> biosys2.exe < t\SAMPLE1.BIO > test.out

TESTING

In the ./t directory are 4 .BIO data files and 4 corresponding .OUT
files. The .BIO files accompanied the original distribution, in
BIOSYS.ZIP. These were evidently formatted for biosys version 1. They
have been modified to work with biosys2.exe. Run biosys2.exe as
described above, and compare the test output to the analogous .OUT
file in the ./t directory.

REFACTORING DETAILS

Some details and notes to myself are contained in the file 
refactor-notes.txt. All the changes made to the original source
can be found in 'unified diff' format in the file changes.dif.

ORIGINAL FILES

The .ZIP files containing the original source are found in 
the ./org directory.

LICENSE
    
    Original source copyright (C) 1997 by William C. Black

    This distribution Copyright (C) 2009 Mark A. Jensen

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details at
    http://www.gnu.org/licenses/.


