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|Interface||Command line interface|
|Restrictions to use||Academic or non-commercial use|
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- person_outline Itay Mayrose
Publication for Rate4Site
Measuring evolutionary rates of proteins in a structural context
[…] AMMA: For amino-acids, use the model specification -m PROTGAMMALG, and for nucleotides use the model specification -m GTRGAMMA.As an alternative method to infer site-wise amino acid rates one can use Rate4Site (or its accompanying webserver, ConSurf ). Rate4Site is a tool for inferring site-wise evolutionary rates in amino acid sequences . Download Rate4Site from https://www.tau.ac.il/~itaymay/cp/ […]
Relative evolutionary rate inference in HyPhy with LEISR
[…] Evolutionary rate inference is a fundamental analysis in computational molecular evolution (). A widely-used tool for inferring evolutionary rates from phylogenetic protein data is Rate4Site, which exists both as a server and a command-line tool (). Although this method has proven extremely useful over the years, garnering nearly 500 citations, Rate4Site has several limitations: […]
Protein protein binding selectivity and network topology constrain global and local properties of interface binding networks
[…] mains in the 56 yeast CME proteins and 127 human ErbB proteins, we collected orthologs of each protein, ran multiple sequence alignments with MAFFT, and analyzed residue conservation with the ConSurf rate4site program (or web-server). To assign a conservation score to each domain, the average over all residues in the domain were taken (Table ). Orthologs were constructed from BLAST searches agains […]
Contrasting patterns of nucleotide polymorphism suggest different selective regimes within different parts of the PgiC1 gene in Festuca ovina L.
[…] le S1) of the acquired homologous sequences was constructed using MAFFT [, ], and this alignment was then used to build a phylogenetic tree using the neighbour-joining algorithm as implemented in the Rate4Site program . The level of evolutionary conservation was then estimated, as a conservation score for each amino acid site using an empirical Bayesian algorithm  implemented in the ConSurf Se […]
Disease associated mitochondrial mutations and the evolution of primate mitogenomes
[…] ned codon position along primate radiation using SLAC in DataMonkey server [,]. Finally, Ind3 reported the standardized evolutionary rates per aligned residue position with ConSurf server [,] using a Rate4Site algorithm under an empirical Bayesian methodology [,]. The Rate4Site algorithm uses the tree topology and branch lengths to calculate rates of amino acid substitutions per site. The resultin […]
A dynamic hydrophobic core orchestrates allostery in protein kinases
[…] ation. A multiple sequence alignment (MSA) of the homologs was constructed using MAFFT (). The MSA was used to build a phylogenetic tree using the neighbor-joining algorithm (), as implemented in the Rate4Site () program. Position-specific conservation scores were computed using the Bayesian algorithm and JTT evolutionary substitution model and were mapped to a single-digit scale from 0 to 9 and p […]
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