Phylogenetics
There are four major methods for constructing phylogenetic trees, and no one approach is clearly preferred in all instances: (1) Distance (including neighbor-joining), (2) maximum parsimony, (3) maximum likelihood, and (4) Bayesian inference.
Regardless of the method, bootstrapping analysis should be performed to assess the robustness of the tree topology.
Regardless of the method, bootstrapping analysis should be performed to assess the robustness of the tree topology.
Tree-building Programs
Seaview performs multiple sequence alignments and can generate the following types of trees (all with bootstrapping analysis): (1) Distance (NJ or BioNJ with options); (2) Parsimony (PHYLIP, using the protpars algorithm); (3) Maximum likelihood (PhyML, with multiple options)
MegAlign Pro (Lasergene) uses the BioNJ distance method to create the tree.
Jalview uses distance methods (including neighbor-joining) to create trees
