As such, eBURST and a maximum parsimony minimum spanning network analyses were carried out.
Phylogenetic analyses were conducted with MEGA version 3.1 software [ 86] using maximum parsimony, minimum evolution, and neighbor-joining methods with the Poisson-correction for multiple amino acid substitutions.
Based on the alignment we created multiple phylogenomic trees (maximum parsimony, minimum evolution, neighbor joining) including 100 bootstrap replicates.
The evolutionary history was inferred using the maximum parsimony, minimum evolution (ME), neighbor-joining (NJ) and unweighted pair-group method with arithmetic mean methods.
The several chloroplast GPx proteins clustered with different proteins in maximum parsimony, minimum evolution and neighborhood joining trees (Fig. 14B; Additional files 9 and 10).
The phylogenetic tree was constructed using four different methods: Neighbor-Joining (NJ), Maximal Parsimony (MP), Minimum Evolution (ME) and Bayesian Inference (BI).
Phylogenetic trees were generated using neighbor-joining, maximal parsimony and Bayesian approaches [ 72- 76].
However, our objective function for the haplotype assembly problem makes the maximal parsimony assumption common in many computational biology problems (Fitch, 1977; Gusfield, 2003).
Whatever the method used (maximum likelihood, maximum parsimony or minimum evolution), no clear evidence of phylogenetic structure was observed, as illustrated with the maximum likelihood analysis.
SAG: Culture Collection of Algae at Göttingen University, Germany (Sammlung von Algenkulturen der Universität Göttingen, Göttingen, Germany); ML: Maximum likelihood; MP: Maximum parsimony; ME: Minimum evolution; NJ: Neighbor joining.
