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

Fig 5

Screenshots from the PhyloBot ancestral library viewer.

The images shown come from the Ancestral Library computed for the CMGC protein family [31]. (A) The library viewer displays an interactive tree for exploring reconstructed protein ancestors. Users select the maximum likelihood tree based on the alignment method and evolutionary model, and then click on ancestral nodes within that tree. (B) PhyloBot gathers summary statistics about every ancestral node. Shown here is the support summary for ancestral Node 401 in the CMGC family, reconstructed using msaprobs and PROTCATLG. The histogram bins the sequence sites of Node 401 according to their amino acid probability support. In this case, a majority of sites have support of 0.9 or greater. The line graph expresses the probability of the maximum likelihood amino acid residue, along with the second-best and third-best reconstructed residues; the line graph is a quick way to visually determine which protein domains were reconstructed with strong support. In this example, there is an unstructured region in the C-terminus that was reconstructed with low support. (C) PhyloBot shows details about every site in every reconstructed ancestor. Shown here is the probability support by site for Node 401 in CMGC. Users can optionally map this data to extant sequences. For example, here a user selected Homo sapiens CDK6. In the table the first column displays the sequence site in the MSAProbs alignment, the second column expresses the site number and best amino acid state in the reconstructed ancestor Node 401, the third column expresses the site number and amino acid state in Homo sapiens CDK6, the fourth column expresses the full probability distribution of all amino acid states reconstructed at that site in Node 401.

Fig 5

doi: https://doi.org/10.1371/journal.pcbi.1004976.g005