Equipe MAB - LIRMM Information Genomique et Structurale
"A la Carte" Mode
Alignment
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Curation
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Phylogeny
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Tree Rendering
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Workflow Settings


Name of the analysis Name length is limited to 20 characters (optional):

Choose processing steps to run and select software to use:

Multiple Alignment:
MUSCLEFastest and good accuracy
ProbConsHigh accuracy but lengthly computational time
T-CoffeeHighest accuracy but lengthly computational time
ClustalWLess accurate than modern programs

Alignment curation:
GblocksUsing default parameters, Gblocks is more stringent than just removing positions with gaps.
Remove positions with gapsThis is a standard, simple option, which can be used instead of the sophisticated GBlocks cleaning program.

Construction of phylogenetic tree:
Maximum LikelihoodHigh robustness of trees but lengthy computational time
PhyML
ParsimonyAdapted to similar sequences
TNT
DistancesFaster
ProtDist/FastDist + BioNJ
ProtDist/FastDist + Neighbor
Bayesian inferenceHigh robustness of trees but highest computational time
MrBayes (limit: 30 sequences)

Visualisation of phylogenetic tree:
TreeDynMost customizable tree, colorization...
DrawgramCladogram or phenogram-like rooted tree
DrawtreeUnrooted tree diagram


Run workflow:

all at onceThe workflow will execute every stage without your intervention. step by stepThe workflow will stop after each stage and you will have to validate the results to process to the next stage.





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