进化分析软件

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: 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

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