Alignment

ClustalW (version 1.83)
Muscle (version 3.52)

  Phylogeny

  Phylip (version Phylip 3.65)
  Resampling
SeqBoot
Consense
  Distances
DnaDist
ProtDist
  Tree reconstruction
Neighbor
Fitch
  Maximum Likelihood
DnaML
ProML
  Parsimony
DnaPars
ProtPars
PhyML (version 2.4.5 aLRT)
TreePuzzle (version 5.2)
MrBayes (version 3.1.12)

  Evolutionary tests

  Model selection

ModelTest (HYPHY) (version HyPhy 1.0)
ProtTest (HYPHY) (version HyPhy 1.0)

  Relative rates tests

RRTree (version 1.1.11)

  Adaptation tests

yn00 (version PAML 4a)
SLR
CodeML (version PAML 4a)  
  Hyphy
Test for site-wise variation in dS (version HyPhy 1.0)
Single Likelihood Ancestor Counting (version HyPhy 1.0)
Weighted Likelihood Ancestor Counting (version HyPhy 1.0)
FEL with dS constant across Sites (version HyPhy 1.0)
FEL with dS varying across Sites (version HyPhy 1.0)

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