fastDNAml is a program that attempts to solve the same problem as the program dnaml (Version 3.3) by Joseph Felsenstein. fastDNAml 1.0 Gary J. Olsen, Department of Microbiology University of Illinois, Urbana, IL gary@phylo.life.uiuc.edu Hideo Matsuda, Mathematics and Computer Science Argonne National Laboratory, Argonne, IL matsuda@mcs.anl.gov Ray Hagstrom, Physics Argonne National Laboratory, Argonne, IL hagstrom@mcs.anl.gov Ross Overbeek, Mathematics and Computer Science Argonne National Laboratory, Argonne, IL overbeek@mcs.anl.gov What is fastDNAml fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program. fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C. DNAML includes the following notice: version 3.3. (c) Copyright 1986, 1990 by the University of Washington and Joseph Felsenstein. Written by Joseph Felsenstein. Permission is granted to copy and use this program provided no fee is charged for it and provided that this copyright notice is not removed. Use uncompress and tar to extract the fast-dnaml.tar.Z archive file, which contains the following. More complete descriptions are included in the "docs" directory. The required files are in subdirectories: docs/ fastDNAml_doc.txt ...... A description of the program and its options fastDNAml_scripts.txt .. Descriptions of a set of Unix shell scripts for invoking program options to_make ................ Instructions for compiling the program VMS/fastDNAml.com ...... A VAX/VMS command file to help run the program VMS/make_VMS.com ....... A VAX/VMS command file to compile the program source/ fastDNAml_1_0_6.c ...... The C language program source code fastDNAml_1_0.h ........ The C language program header file scripts/ .................. A directory with 28 shell scripts described in fastDNAml_scripts.txt testdata_6/ ................ A directory of test data input files and corresponding output files Note: FastDNAml is clocked at about 15 times faster than dnaml version 3.3, on a Sun Sparcstation with sun compilers. dnaml version 3.4 is faster than 3.3