Mac5

Background

MAC5 is a program which implements MCMC sampling to estimate a phylogenetic tree from a DNA multiple alignment. What differentiates MAC5 from similar programs (e.g. BAMBE, MrBayes) is its use of five-state sequence evolution models as a means to include the gap information when estimating an alignment. Despite vilification of these models in the literature in the past (e.g., Durbin et al., 1998, p. 217), we have found that, in many circumstances, they are useful for improving the precision of topology estimation.   The Mac5 distribution is available for several platforms:

• Unix: the preferred distribution due to the computational demands, Mac5 is available as a source tarball, and so should only be used by those comfortable with compiling and installing Unix software. This distribution includes the source, makefiles and project files for CodeWarrior.
• Macintosh: Mac5 may be compiled for Mac OS X using the above Unix tarball. Otherwise a simple console versions (as a self-extracting archive) is available that will run on OS X and 9.
• Windows: Simple console versions (as a zipped archive) are available that will run on Windows. This version has been only been tested lightly.

Mac5 was produced with the aid of the BBSRC (Biotechnology and Biological Sciences Research Council UK).   Note that due to life changes and the development of other software, Mac5 is no longer being developed and is not supported.

Usage

Documentation for Mac5 can be found in the distribution.