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Branch support values are approximate likelihood ratios (aLRs), expressing the ratio of the likelihood of the maximum likelihood phylogeny to the next-best phylogeny lacking the indicated branch.
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Further analysis was aimed at detection of functional classes whose genes mainly underwent positive selection on the indicated branches (Additional data file 3).
▪ Full lines indicate branch lengths.
Figure 1 shows a tree indicating branch points marked by the different chlamydiae group-specific proteins.
Nevertheless, they differed in relative branch lengths indicating branch specific rates of evolutionary change of the TLR2 protein sequence.
Numbers below each partition name represent optimal treelength for clade in left-most column; column "WO" indicates optimal treelength without that clade; column "BS" indicates branch support for that clade from partition (i.e., partition WO - partition).
The topologies of the NJ, ML and Bayesian trees were almost identical; therefore, we present a phylogenetic tree with ML bootstrap (BS) values and Bayesian PP indicating branch support (Fig. 3A).
However, the topologies of the ML, unpartitioned Bayesian and partitioned Bayesian trees were congruent, therefore we present the optimal ML tree (-ln L = 14501.43296) with ML bootstrap (BS) values and unpartitioned Bayesian posterior probabilities (PP) indicating branch support.
Round brackets '(' and ')' indicating branches.
Red lines indicate branches with losses; green lines indicate branches with gains.
Arrows indicate branches being pruned while arrowheads point to growing branches.
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