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ProtEvol

    The program ProtEvol performs two kinds of computation:

    1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference. Citation: Arenas, Sanchez-Cobos and Bastolla, Maximum likelihood phylogenetic inference with selection on protein folding stability, preprint.

    2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding. It implements three selection models:
      1. Neutral;
      2. Based on the fixation probability of the Moran process, which depends on the difference of logarithmis fitness and on effective population size.
      3. Based on the mean-field stationary distributions computed at the previous point.

  • Usage and installation Documentation included with the package.
  • License : Free use for Educational and Research Purposes.
  • Contact : ub@cbm.uam.es
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