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. 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. The programs are described in the document paml.ps (postscript); use lpr paml*.ps to get a hard copy. Bug fixations since the preparation of the document are recorded in the file paml.release. Excutables in the PowerMac version uses "infile" as the sequence file name, while the DOS version runs in the same way as the UNIX version. Documents and example files are not included in the DOS or MAC archives. 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). After getting the file paml1.1c.tar.Z, you should use the following commands to decode it: uncompress paml1.1c.tar.Z tar xf paml1.1c.tar I used the following commands to archive and compress the files: tar cf paml1.1c.tar * compress paml1.1c.tar PAML is distributed free of charge for academic use only. Comments and suggestions are appreciated. 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