Rate4Site protocols

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chevron_left Phylogenetic inference Multiple amino acid sequence alignment Structure conservation prediction chevron_right
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Rate4Site specifications

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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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Maintainer


  • person_outline Itay Mayrose <>

Publication for Rate4Site

Rate4Site in pipelines

 (2)
2017
PMCID: 5384802
PMID: 28435869
DOI: 10.1126/sciadv.1600663

[…] 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 […]

2008
PMCID: 2475510
PMID: 18670631
DOI: 10.1371/journal.pgen.1000146

[…] score in the (50–55) loop of the protein. evolutionary rates were calculated using the conservation scores for each amino acid position in the multiple sequence alignment were computed using the rate4site program . the bayesian method was applied for the calculation of the conservation scores using the jones-taylor-thornton amino acid substitution model . the conservation scores computed […]


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Rate4Site in publications

 (63)
PMCID: 5676193
PMID: 29167739
DOI: 10.5256/f1000research.13954.r27048

[…] calculate evolutionary rates, hyphy’s fel and leisr approaches. as an alternative method to measuring amino acid evolutionary rates with leisr, we presented a brief pipeline in the notes that uses rate4site software. other methods for calculating evolutionary rates have been provided by rodrigue et al. and tamuri et al. – , whose methods infer codon-level site-wise evolutionary rates […]

PMCID: 5797227
PMID: 29396449
DOI: 10.1038/s41598-018-20231-5

[…] extent monopolar and bipolar cytokinesis specific phosphosites are evolutionary conserved. the conservation scores of each site, on a scale from 9 (the most conserved) to 1, were calculated using rate4site. strikingly, those phosphopeptides that are common to both monopolar and bipolar cytokinesis are the most conserved ones. the distribution of the phosphopeptides in this category is skewed […]

PMCID: 5786331
PMID: 29338055
DOI: 10.1371/journal.ppat.1006826

[…] scored and clustered resulting in 10 models for each of three scoring methods (interevscore, soap_pp atom-based statistical potential, and frodock). conservation of residues was assessed with the rate4site., procedures for the index case have already been described []. all other procedures were performed under protocols approved by the institutional review board at case western reserve […]

PMCID: 5766984
PMID: 29344086
DOI: 10.1186/s13068-017-1006-7

[…] was selected. the gh7 cbh catalytic domains were realigned by clustalw using mega7 software [], followed by indel elimination. this alignment was analyzed by rca as described earlier []. in short, rate4site (version 2.01) was used to calculate the degree of conservation (s score) for each amino acid position using the empirical bayesian method [, ]. a sliding window-average (n = 7) s score […]

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

[…] (likehood estimation of individual site rates, pronounced “laser”), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in hyphy. leisr is based on the popular rate4site () approach for inferring relative site-wise evolutionary rates, primarily from protein data. we extend the original method for more general use in several key ways: (i) we increase […]


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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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