The phylogeny was inferred using the Maximum Parsimony method as described in the methods.
Figure 4 Phylogenetic tree based on tuf gene sequences of ChIF phytoplasma and related 17 phytoplasmas, constructed by the maximum parsimony method.
The phylogeny was inferred using the Maximum Parsimony method [42].
The evolutionary history of the yqi gene was inferred using the Maximum Parsimony method.
The evolutionary history was inferred using the flat-weighted Maximum Parsimony method.
For concatenated housekeeping alleles, evolutionary history was inferred using the NJ method or maximum parsimony method (PAUP 4.0).
Construction of phylogenetic trees and divergence analysis was performed by maximum parsimony method using MEGA 4 software (Molecular Evolutionary Genetics Analysis) [26].
The AA node sequences were estimated on this tree by applying an extended maximum parsimony method which reduces uncertainty due to convergent evolution [35].
Phylogenetic trees were constructed by maximum parsimony method from aligned sequences or by using a maximum likelihood method from the best model identified by Modeltest 3.7.
The node sequences in Figures 3 & 4 and Tables 1 & 2 were estimated by applying the extended maximum parsimony method at the DNA level to the three local lineages of Primates, Cetartiodactyla, and Afrotheria.
For the later, both the Neighbor-Joining method (with Kimura 2-Parameter and Tamura-Nei models) and the Maximum Parsimony method (using the max-min branch-and-bound algorithm) were used as previously described [21].
