By Michael Robeson
ARB
Clustalx
DNASTAR
GBlocks
Greengenes
MAFFT
Malign
Muscle
ProAlign
PROBCONS
Se-Al
SeaView
Sequencher
SILVA Aligner
Staden
STRAP
Squint
XCED
4Peaks
FinchTV
EditView
ATV
BAOBAB
Dendroscope
FigTree
HyperTree
NJPlot
Paloverde
Topiary Explorer
TreeDyn
TreeEdit
TreeGraph
TreeIllustrator
TreeView
BioMatters
CLC Main Workbench
MacGDE
MEGA
Mesquite
ModelGenerator
ModelTest
MrModelTest
MultiPhyl
PROTTEST
ANCML
BAli-Phy
BAMBE
BEAST
Clann
Clearcut
FastTree
GARLI
HYPHY
LVB
MacClade
MLTreeMap
MrBayes
Notung
PAUP*
Pebble
PHASE
PHYLIP
PhyloCoco
Phylo_win
PhyloBayes
PhyML
phyutility
POY
r8s
RAxML
RAxML EPA
SIMMAP
SplitsTree
TNT
Treefinder
BAPS
Circuitscape
FastUniFrac
GenoDive
Mothur
Phylocom
QIIME
Structure
UniFrac
Xserve Image by Apple, Inc
AmplifX
BioSAVE
Biovolution
BlastViewer
DatabaseViewer
DNA Artist
DNA to Protein
DivergentSet
eBiotools
EMBOSS
EnzymeX
GO-Getter
KoriBlast
Mallard
McClellan Lab
Oxford E. Bio.
PinTail
Sequence Analysis
Sergio Links
XplorSeq
Fink
DarwinPorts
MacPorts
MacResearch
BioPython
matplotlib
PyCogent
Python
SciPy
MEME
MotifCluster