Boostrap support (% of 1,000 bootstrap replicates) was calculated using the neighbor-joining, minimum evolution, and maximum parsimony methods.
Phylogenetic trees were constructed for cyt b and COI sequence alignments using the Maximum Parsimony, Neighbor-Joining, Minimum Evolution and Maximum Likelihood methods.
Full phylogenetic trees for Maximum Parsimony, Neighbor-Joining, Minimum Evolution and Maximum Likelihood methods for the COI and cyt b genes can be found in the Figures S1 S11 and Tables S3 and S4.
It has been previously explored that MrBayes3.1 with appropriate constraints, produced trees with higher confidence at each node than other tree methods: neighbor-joining, minimum evolution, maximum parsimony, and the un-weighted pair group method with arithmetic mean [61].
Geneious Software was used to estimate phylogeny with the neighbour-joining, minimum evolution, or maximum parsimony method.
Neighbor-Joining, Minimum Evolution, Maximum Parsimony, UPGMA Unweighted Pair Group Methodd with Arithmetic mean) and Bayesian methods of phylogeny estimation were utilized [ 28].
This was found in all phylogenetic trees created whether using neighbour-joining, minimum evolution or maximum parsimony on both nucleotide and protein sequences.
Phylogenetic analysis was performed with the program package MEGA4 [ 107] using neighbor-joining, minimum evolution and maximum parsimony algorithms and bootstrapping with 500 replicates.
Using different phylogenetic reconstructions (neighbor-joining, minimum evolution and maximum parsimony) we obtained the same tree topologies where the animal isolates are basal and the human isolates are derived, suggesting a zoonosis scenario for C. pneumoniae (figure 3).
Neighbor-Joining, Minimum Evolution and Maximum Parsimony phylogenetic analyses were performed on amino-acid and nucleotide sequences of various datasets (six LGR proteins with or without related proteins identified by BLAST; either whole proteins or their LRR or non-LRR domains) with the same software using p-distance and the complete deletion option.
