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Impact of phylogeny on the inference of functional sectors from protein sequence data
Fig 4
Impact of phylogeny on mutational effect recovery.
The recovery of the mutational effect vector 
(see Methods) for specific eigenvectors is shown as a function of the number μ of mutations per branch, using ICOD, covariance, SCA and conservation. For ICOD (resp. SCA), eigenvectors associated to the largest eigenvalue Λmax (resp. λmax) are considered. For covariance C, eigenvectors associated to the smallest eigenvalue λmin are considered. Datasets of M = 2048 sequences of length L = 200 were generated along a perfect binary tree with 11 generations, using various numbers μ of accepted mutations per branch. As in Fig 3, we employed the mutation acceptance criterion in Eq 2 with 
and τ* = 90. We used the same vector of mutational effect 
as in Fig 2 and Fig 3. All results are averaged over 100 realisations of data generation. The null model corresponds to recovery from a random vector (see Methods, Eq 13).
doi: https://doi.org/10.1371/journal.pcbi.1012091.g004