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Rate4Site specifications

Information


Unique identifier OMICS_06940
Name Rate4Site
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Maintainer


  • person_outline Itay Mayrose

Publication for Rate4Site

Rate4Site citations

 (62)
library_books

Measuring evolutionary rates of proteins in a structural context

2018
F1000Res
PMCID: 5676193
PMID: 29167739
DOI: 10.5256/f1000research.13954.r27048

[…] 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/ […]

library_books

Relative evolutionary rate inference in HyPhy with LEISR

2018
PeerJ
PMCID: 5804317
PMID: 29423346
DOI: 10.7717/peerj.4339

[…] 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: […]

call_split

Protein protein binding selectivity and network topology constrain global and local properties of interface binding networks

2017
Sci Rep
PMCID: 5514078
PMID: 28717235
DOI: 10.1038/s41598-017-05686-2
call_split See protocol

[…] 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 […]

call_split

Contrasting patterns of nucleotide polymorphism suggest different selective regimes within different parts of the PgiC1 gene in Festuca ovina L.

2017
Hereditas
PMCID: 5437402
PMID: 28529468
DOI: 10.1186/s41065-017-0032-6
call_split See protocol

[…] 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 […]

library_books

Disease associated mitochondrial mutations and the evolution of primate mitogenomes

2017
PLoS One
PMCID: 5433710
PMID: 28510580
DOI: 10.1371/journal.pone.0177403

[…] 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 […]

library_books

A dynamic hydrophobic core orchestrates allostery in protein kinases

2017
Sci Adv
PMCID: 5384802
PMID: 28435869
DOI: 10.1126/sciadv.1600663

[…] 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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Rate4Site institution(s)
Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel

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