- We shall use PAUP*4.0 (PAUPstar). Available from Sinauer Associates, costs US$50 per copy (US$150 for the UNIX version). See: http://lms.si.edu (Laboratory of Molecular Systematics).
- PAUP is available on all computer systems (Macintosh, Windows, UNIX). Only the Macintosh version has a Graphical User Interface (GUI), all the other versions are command-line.
- Written by David Swofford at the Smithsonian Institute, Washington, DC, USA.
PAUP has implemented 3 criteria:
Maximum
Parsimony
Maximum
Likelihood
Distance
Matrix
PAUP has 3 tree-searching
algorithms
Heuristic
Branch-and-bound
Exhaustive
PAUP has 3 algorithms for constructing a tree without searching tree space
Neighbor-Joining
Quartet
Puzzling
Star
decomposition
For a description of terms, see the Glossary.