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Phylogeny Analysis
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Blast: Sequence Explorer
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Blast
BLAST
Multiple Alignment
MUSCLE
T-Coffee
3DCoffee / Expresso
ClustalW
ProbCons
Phylogeny
PhyML
TNT
BioNJ
MrBayes
Neighbor
FastME
ASTRAL
Tree Viewers
TreeDyn
Drawgram
Drawtree
ATV (A Tree Viewer)
Utilities
Gblocks
Jalview
Readseq
Built-in converter
Built-in Curer
SMS
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"A la Carte" Mode
Alignment
MUSCLE
Curation
Gblocks
Phylogeny
PhyML
Tree Rendering
TreeDyn
Help
1. Workflow Setup
Workflow Settings
Name of the analysis
(optional):
Choose processing steps to run and select software to use:
Multiple Alignment:
MUSCLE
T-Coffee
3DCoffee
ClustalW
Alignment curation:
Gblocks
Remove positions with gaps
Construction of phylogenetic tree:
Maximum Likelihood
PhyML
Parsimony
TNT
Distances
ProtDist/DnaDist + BioNJ
ProtDist/DnaDist + Neighbor
Visualisation of phylogenetic tree:
TreeDyn
Drawgram
Drawtree
Additional methods
Multiple Alignment
ProbCons
Phylogeny
FastME
MrBayes
FastME includes tree refinement; it is a separate method from BioNJ and Neighbor.
Run workflow:
all at once
step by step