Software

Second Edition

http://evolution.genetics.washington.edu/phylip/software.html

created using wordle.net

HyPhy: http://www.hyphy.org/

PAUP*: http://paup.csit.fsu.edu/

BEAST: http://beast.bio.ed.ac.uk/

SplitsTree: http://www.splitstree.org/

MrBayes: http://mrbayes.csit.fsu.edu/

MEGA: http://www.megasoftware.net/

Tree-Puzzle: http://www.tree-puzzle.de/

RDP3: http://darwin.uvigo.es/rdp/rdp.html

Datamonkey: http://www.datamonkey.org/

IQPNNI: http://www.cibiv.at/software/iqpnni/

Tracer: http://tree.bio.ed.ac.uk/software/tracer/

FigTree: http://tree.bio.ed.ac.uk/software/figtree/

DAMBE: http://dambe.bio.uottawa.ca/software.asp

Consel: http://www.is.titech.ac.jp/~shimo/prog/consel/

ProtTest: http://darwin.uvigo.es/software/prottest.html

PAML: http://abacus.gene.ucl.ac.uk/software/paml.html

Alignment software (see table): Clustal, Muscle, T-Coffee

ModelTest: http://darwin.uvigo.es/software/modeltest.html

Simplot: http://sray.med.som.jhmi.edu/SCRoftware/simplot/

Phylip: http://evolution.genetics.washington.edu/phylip.html

TreeView: http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

Lamarc: http://evolution.genetics.washington.edu/lamarc/index.html

more software at:

Philippe Lemey

Table of contents

A Practical Approach to phylogenetic analysis and hypothesis testing

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