paml.readme
-----------

PAML (for Phylogentic Analysis by Maximum Likelihood) contains three
main programs for model fitting and phylogenetic tree reconstruction
using nucleotide or amino-acid sequence data.  The programs were
written in ANSI C and tested on UNIX systems, although MAC and
PowerMac excutables are also available.  We do not have any PCs in the
lab, and so I have not compiled the program for DOS systems.  The UNIX
commands for compiling the programs using the GNU gcc compiler and the
SUN acc compiler are listed in two files named paml.gcc and paml.acc,
respectively.  Type "source paml.gcc" or "source paml.acc" for
compiling.  A document, paml1_2.doc, is prepared using Microsoft Word
6.0 for the Mac (with Equation Editor 2.0), which is supposed to be
compatible with Microsoft Word 6.0 for Windows, although I had reports
that suggest otherwise; if you cannot print out the document, I can
send you a copy by mail.

The package can be obtained from ftp.bio.indiana.edu (129.79.225.25)
under the subdirectory Incoming/ or molbio/evolve by anonymous ftp
(binary), or from our ftp site at mw511.biol.berkeley.edu/pub.
Currently C source code (paml1.2.tar.Z), MAC (paml1.2.68K.sea.bin) and
PowerMac (paml1.2.PPC.sea.bin) executables are available.  The Unix
compressed archive should be decoded using the following commands:

             uncompress paml1.2b.tar.Z
             tar xf paml1.2b.tar

PAML is distributed free of charge for academic use only.  Complaints
and suggestions are welcome. 

Ziheng Yang

Department of Integrative Biology      Email: ziheng@mws4.biol.berkeley.edu
University of California               Phone: (510) 643 6299
Berkeley, CA 94720-3140                Fax:   (510) 643 6264
http://mw511.biol.berkeley.edu/ziheng/ziheng.html
http://mw511.biol.berkeley.edu/ziheng/paml.html