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

Fig 3

Example of alignment robustness analysis.

In this simple example, orthologous amino acid sequences from five species were aligned using three different methods for multiple sequence alignment: Muscle, MSAProbs, and MAFFT. (A) PhyloBot maps the aligned position of every character across all alignments. Shown in red is the character map for the amino acids aligned into site 3 of the Muscle alignment. In the MSAProbs sequence alignment, these same residues are split across sites 3 and 4. In the MAFFT alignment, these residues are split across sites 3, 4 and 5. (B) PhyloBot displays the character map as pie charts expressing site identity relative to the Muscle alignment. PhyloBot will also show these maps relative to MSAProbs and MAFFT alignments.

Fig 3

doi: https://doi.org/10.1371/journal.pcbi.1004976.g003