Table 2

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


Gonnet BMC Bioinformatics 2012 13:148   doi:10.1186/1471-2105-13-148

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