The program ProtEvol performs two kinds of computation:
Usage and installation Documentation included with the package.
License : Free use for Educational and Research Purposes.
Contact : firstname.lastname@example.org
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- 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
Citation: Arenas, Sanchez-Cobos and Bastolla, Maximum likelihood
phylogenetic inference with selection on protein folding stability,
- 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
- Based on the fixation probability of the Moran process,
which depends on the difference of logarithmis fitness and
on effective population size.
- Based on the mean-field stationary distributions computed at
the previous point.
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