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Paup

Phylogenetic Analysis using Parsimony

Introduction

Paup image

This program is the most important program for those who wish to reconstruct phylogenetic relationships. It is a stand-alone program and runs on Apple macintosh™, Windows™ and UNIX operating systems. It can deal with DNA and protein sequences as well as morphological data or any binary or multistate character data. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees.


Paup analyzes
  • Molecular sequences
  • Morphological data
  • Other data types
Using
- Maximum likelihood
- Parsimony
- Distance methods

More about the Unix version of Paup

The "Portable Version" of PAUP* 4.0 is written and will be distributed in ANSI C. PAUP* will run on most platforms (architecture/OS) provided the source is compiled using an appropriate C compiler. Note: PAUP* 4.0 Portable Version does not print or save high-resolution trees. To print graphical trees we recommend the program TreeView by Rod Page.
Before the final release of Version 4.0 we are making a set of UNIX/VMS beta executables available for the following platforms:
- Alpha/Unix (OSF1, Digital UNIX, Tru64 UNIX)
- Alpha/VMS
- Alpha/Linux
- PPC/Linux
- PPC/Mac OS X (this is not a carbonized application; it is command-line only)
- RS6000/AIX
- SGI/Irix (MIPS II and MIPS III)
- SPARC - UltraSPARC/Solaris
- x86/Linux
- Possibly others on request
Once the final version is completed, support for more platforms will be provided. Requests for new orders should contact Sinauer Associates, Inc.

All this and more information can be found on the Paup homepage



Reference documents

Paup 4.0 Beta documents contains two documents. The first one is the command reference guide, while the second one is the Quick Start tutorial.

Click here to look at the sample analysis files of Paup

Here is the Sample NEXUS data Paup sample NEXUS data

Here is the sample import data Paup sample import data
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