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WETE: a web interface of the ETE3 build function for sequences alignment and phylogenetic tree reconstruction

Aligners :

mafft_default: mafft alignment with default parameters

mafft_einsi: mafft alignment using the E-INS-i mode

mafft_linsi: mafft alignment using the L-INS-i mode

mafft_ginsi: mafft alignment using the G-INS-i mode

clustalo_default: clustalo with default parameters

muscle_default: muscle alignment with default parameters

Alignments cleaners:

trimal001: trimal alignment cleaning removing columns with >1% gaps

trimal01: trimal alignment cleaning removing columns with >10% gaps

trimal02: trimal alignment cleaning removing columns with >20% gaps

trimal03: trimal alignment cleaning removing columns with >30% gaps

trimal05: trimal alignment cleaning removing columns with >50% gaps

trimal_gappyout: trimal alignment cleaning using gappyout algorithm

Model testers:

prottest_default: Uses BioNJ trees to select best protein model from: JTT, WAG, VT, LG and MtREV. Fixed parameters: +G+I+F

pmodeltest_full_ultrafast: Test all models using NJ tree inference and skipping gamma, invariant sites, and frequency site estimations (!G!I!F)

pmodeltest_full_fast: Test all models using NJ tree inference

pmodeltest_full_slow: Test all models using ML tree inference

pmodeltest_soft_ultrafast: Test JTT,WAG,VT,LG,MtREV models using NJ tree inference and skipping gamma, invariant sites, and frequency site estimation (!G!I!F)

pmodeltest_soft_fast: Test JTT,WAG,VT,LG,MtREV models using NJ tree inference

pmodeltest_soft_slow: Test JTT,WAG,VT,LG,MtREV models using ML tree inference

Tree builders:

bionj_default: BioNJ tree inferred with Phyml. Default models JTT/GTR

fasttree_default: Fasttree with default parameters. Default models JTT+CAT/GTR+CAT

fasttree_full: Fasttree with slow NNI and MLACC=3. Default models JTT+CAT/GTR+CAT

phyml_default: Phyml tree using +G+I+F, 4 classes and aLRT branch supports. Default models JTT/GTR

phyml_default_bootstrap: Phyml tree using +G+I+F, 4 classes and 100 bootstraps. Default models JTT/GTR

raxml_default: RAxML with default parameters, GAMMA JTT/GTR and aLRT branch supports.

raxml_default_bootstrap: RAxML with default parameters, GAMMA JTT/GTR and 100 bootstrap replicates

iqtree_default: IQ-TREE with no model specified (MFP by default) and 1000 replicates for SH-aLRT

iqtree_bestmodel: IQ-TREE with TESTNEWONLY for model finder and 1000 replicates for SH-aLRT

iqtree_C10: IQ-TREE with CAT profile mixture model C10 and 1000 replicates for SH-aLRT

iqtree_C30: IQ-TREE with CAT profile mixture model C30 and 1000 replicates for SH-aLRT

iqtree_C60: IQ-TREE with CAT profile mixture model C60 and 1000 replicates for SH-aLRT