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It simulates protein evolution subject to the constraint of.

Phylogenetic inference with selection on protein folding stability, Used together with the site-specific distributions for applications inĬitation: Arenas, Sanchez-Cobos and Bastolla, Maximum likelihood

The program also computes an exchangeability matrix derived from anĮmpirical substitution model or from a mutation model that can be State of the protein against both unfolding and misfolding. That have minimal differences with respect to the backgroundĭistribution and that constraint the average stability of the native It computes the mean-field site-specific amino acid distributions.The program ProtEvol performs two kinds of computation: References : Lupyan D, Leo-Macias A, Ortiz AR (2005) Bioinformatics (2005) 21, 3255-63.Providing a common 3D superimposition, a corresponding structure-based sequence alignment andĪ dendrogram for the set of structures aligned. MAMMOTH-mult is a multiple alignment version of MAMMOTH. References : Ortiz AR, Strauss CE, Olmea O (2002) Protein Sci.

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Version : Free use for Educational and Research Purposes.

Structures to a query structure in a database.

It alsoĪllows the comparison of two experimental structures, or the search for similar

Protein structure with an arbitrary low-resolution protein tertiary model. It allows the comparison of an experimental MAMMOTH (Matching Molecular Models Obtained from Theory) is a sequence-independent References : Pascual-García A, Abia D, Méndez R, Nido GS, Bastolla U.Version : 1.0 Free use for Educational and Research Purposes.The first line may be PDBDIR= (default: current directory). Input: alignment file in fasta format with names of pdb files as file names, optionally followed by the chain index (Ex: >1opd.pdb A) 2010) and the TM-score (Zhang and Skolnick 2005) divergence -log(TM). The contact divergence (Pascual-Garcia et al. Given a multiple sequence alignment, for all pairs of proteins it computes the Tajima-Nei sequence divergence,

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