BioAfrica - Bioinformatics in Linux and PAUP *

Bioinformatics in Linux and PAUP *:

The program Phylogenetic Analysis Using Parsimony and other methods (PAUP*) has made it the most widely used software package for the inference of evolutionary trees. With the inclusion of maximum likelihood and distance methods in PAUP* 4.0, the new version is the most complete software for phylogenetic analysis... For more information go to the PAUP* official pages.

Users access the Linux version of PAUP* 4.0 may use the command-line interfaces or the GDE menu-driven interface developed by Eric Linton to implement all of the available functions. Also PAUP scripts developed by Marco Salemi for many phylogenetic methods (parsimony, distance and likelihood) is available for download in our website. These scripts inclue most of the nucleotide substitution models to produce fine maximum lkelihood trees.

PAUP * Menu-Driven Interface for the Genetic Data Environment (GDE):

The GDE-PAUP menu is a user friendly interface to access most of the available PAUP*functions.
It was Created by Eric W. Linton - lintone@msu.edu - Michigan State University, during the Workshop on Molecular Evolution at Woods Hole Marine Lab. in 1996. Last revised in January 2003.

Download the PAUP* 4.0 menu file for GDE.

Download the Modeltest 3.1 menu for GDE.

Download the Instructions for setting up the menus on GDE for Linux.

Screenshots of the Menu interface:

GDE need to be running in your machine before you attempt to setup the PAUP* menu.

Download page for GDE for Linux.

Scripts for Advanced Phylogenetic Analysis under PAUP *:

The files for download are a set of NEXUS scripts to create fine distance and likelihood trees.
It was Created by Marco Salemi, University of California-Irvine and the Rega Institute at the Catolic University of Leuven, Belgium. Last revised in January 2003.

Felsenstein 81 (F81)
dynamweight+F81G.nex

Tamura-Nei (TrN)
dynamTRng+SPR.nex
dynamTRngI+SPR.nex
dynamTRngI+NNI+TBR.nex

Haseqewa-Kishino-Yano (HKY 1985)
dynamHKYig+SPR.nex
dynamHKYg+NNI+TBR.nex
dynamHKYig+NNI+TBR.nex

Tranversion Model (TVM)
dynamweight+TVMig.nex

dynamTVMig+NNI+TBR.nex

General Time Reversible (GTR)
dynamREVig+SPR.nex

dynamREVig+NNI+TBR.nex

Instructions for using the scripts in PAUP*.

Descriptions of nucletide substitution models are available from the Workshop of Molecular Evolution at Woods Hole.

The Phylogenetic Handbook : A Practical Approach to DNA and Protein Phylogeny - This book contains an extensive practical section written by the PAUP* author David Swofford.