PAUP* Scripts

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 Florida-Gainsville and Tulio de Oliveira, Africa Centre for Health and Population Studies, University of kwaZulu-Natal.

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.

Page last updated by Tulio de Oliveira.