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PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories

Fig 4

Example of ancestral node robustness analysis.

In this small example with protein sequences from five species, maximum likelihood phylogenies were inferred using four different evolutionary models (JTT+GAMMA, JTT+CAT, LG+GAMMA, and LG+CAT) based on three different sequence alignment methods (Muscle, MSAProbs, and MAFFT). The resulting ML phylogenies disagree in their topologies, and an ancestral node in one tree may not exist in other trees. For example, shown in red is the phylogenetic node corresponding to the most-recent ancestor of H. sapiens, M. musculus, and G. gallus, with X. tropicalis and T. teleost as the outgroup. This ancestral node is not inferred to exist when using some combinations of models and methods. Specifically, the alternate phylogenies support an evolutionary hypothesis in which the sequences from G. gallus and X. tropicalis are sister to each other. PhyloBot gathers this information about all reconstructed ancestral nodes, in order to assess the extent to which an ancestor’s existence is robust across different models and methods.

Fig 4

doi: https://doi.org/10.1371/journal.pcbi.1004976.g004