BioAfrica - PAUP* Basic Commands for Distance Tree

Action for Building Capacity (ABC) Fogarty Workshops:
Introduction to HIV Sequencing and Phylogenetic Analysis.
9 to 13 of February 2004, Durban, South Africa.

Basic Commands for PAUP*
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Basic Commands for Distance-NJ tree construction:

Log file=alinhamento.log;
(create a log file named: alinhamento.log)

showmatrix;
(used to check the name of sequences).

Set criterion=distance;

(setup the analysis to distance)

Dset distance=F84;
(setup the distance matrix to F84)

outgroup OCM91MVP5180;

(uses as outgroup the sequence OCM91MVP5180)

NJ;

(Do Neighbour-Joining command)

Savetree brlens=yes file=alinhamentoO.tre;

(Save the phylogenetic tree with branch lenghts to file named alinhamentoO.tre)

Bootstrap nreps=100;

(Perfom bootstrap analysis with 100 replicates)

Commands questions (examples):

set ?;
dset ?;
savetree ?;

More information on PAUP* commands

Book: The Phylogenetic handbook (With a full chapter by the PAUP* creator - David Swofford).
PAUP* forum.
PAUP* scripts for phylogenetic analysis - BioAfrica.

Sponsors:

Fogarty ABC Training program:

Tufts-New England
Medical Center

Africa Centre for Health and Population Studies ABC program

The Nelson R Mandela School of Medicine

The Wellcome Trust

The BioAfrica web site is maintained by: Dr. Tulio de Oliveira,