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, |
alignment | Â |
| Â | Poa, Prank, Probabilistic, Probcons, |
| Â | Prograph |
Methods on MSAs | Gap, Parsimony, PhyML, RAxML, RAxMLG |
Pairwise alignments | GlobalCodonPAM, GlobalJTT, GlobalLG, |
| Â | GlobalSynPAM, GlobalWAG, GlobalGCB, |
| Â | LocalCodonPAM, LocalJTT, LocalLG, |
| Â | LocalSynPAM, LocalWAG, LocalGCB, |
| Â | LogDelGlobal, LogDelLocal |
Pairwise alignments | CodonDist, InducDist |
from MSAs | Â |
Distance methods | BioME, BioNJ, FastME, LST, NJ |