Table 2

Classification of component methods of the PTMS (see methods for full details)
Description Methods
Multiple sequence ClustalO, ClustalW, Mafft, PartialOrder,
alignment
Poa, Prank, Probabilistic, Probcons,
Prograph
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

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

Open Data