Computational protocol: Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

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Protocol publication

[…] Using Muscle [] (default parameters), we aligned the 1971 families, concatenated the variable sites of all alignments and obtained a phylogenetic tree using PhyML [] (100 bootstraps, otherwise default parameters) that we rooted by separating the pestis from the pseudotuberculosis clades, according to a consensus in the literature. In our tree the branch separating the two clades is well supported, as well as the branches surrounding the ancestor that we wish to reconstruct (see Figure ). This step corresponds to part B in Figure . [...] All gene families sequences were then aligned using Prank [] and one gene tree per family was computed using PhyML (100 bootstraps, otherwise default parameters). Because we are aligning recently diverged strains of the same organisms [], the sequences often have not diverged enough to allow an unambiguous tree reconstruction. So we collapsed all branches with a support lower than 99 and then used ProfileNJ [] to solve the created polytomies. ProfileNJ reconstructs species tree branches instead of collapsed branches and chooses among several solutions with a Neighbor-Joining formula. Distances for the Neighbor-Joining part were computed with bppdist, a Bio++ suite software [] (GTR + Γ(4) model).ProfileNJ also roots the gene trees according to "Last Common Ancestor" reconciliation method, annotating internal nodes with duplications or speciations, and choosing a root minimizing the number of duplications.Reconciled gene trees depict the history of the gene family, including all ancestral genes, uniquely defined by the reconciliation.This step corresponds to part C in Figure . […]

Pipeline specifications

Software tools MUSCLE, PhyML, Bio++
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Yersinia pestis, Bacteria
Diseases Yersinia Infections