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Table 2 Classification of component methods of the PTMS (see methods for full details)

From: Surprising results on phylogenetic tree building methods based on molecular sequences

Description Methods
Multiple sequence ClustalO, ClustalW, Mafft, PartialOrder,
  Poa, Prank, Probabilistic, Probcons,
Methods on MSAs Gap, Parsimony, PhyML, RAxML, RAxMLG
Pairwise alignments GlobalCodonPAM, GlobalJTT, GlobalLG,
  GlobalSynPAM, GlobalWAG, GlobalGCB,
  LocalCodonPAM, LocalJTT, LocalLG,
  LocalSynPAM, LocalWAG, LocalGCB,
  LogDelGlobal, LogDelLocal
Pairwise alignments CodonDist, InducDist
from MSAs  
Distance methods BioME, BioNJ, FastME, LST, NJ