ArticlePeerJ2018
Relative evolutionary rate inference in HyPhy with LEISR.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Longer-lived mammals exhibit greater evolutionary conservatism and epigenetic modification at cancer-associated loci.Nature communications · 2026Article
- Accurate prediction of substitution rates at protein sites with a mutation-selection model.Scientific reports · 2025Article
- Comparative genomics uncovers evolutionary drivers of locust migratory adaptation.BMC genomics · 2025Article
- Improved prediction of site-rates from structure with averaging across homologs.Protein science : a publication of the Protein Society · 2024Article
- Dissecting protein domain variability in the core RNA interference machinery of five insect orders.RNA biology · 2021Article
- Site-Specific Amino Acid Distributions Follow a Universal Shape.Journal of molecular evolution · 2020Article
- The evolution of metabolism: How to test evolutionary hypotheses at the genomic level.Computational and structural biotechnology journal · 2020Review
- HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.Molecular biology and evolution · 2020Article
- Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature.Evolution; international journal of organic evolution · 2018Article
- Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function.Molecular biology and evolution · 2018Article
- Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model.Molecular biology and evolution · 2018Article
- Measuring evolutionary rates of proteins in a structural context.F1000Research · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
We introduce LEISR (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 (Pupko et al., 2002) 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 the support for nucleotide data with additional models, (ii) we allow for datasets of arbitrary size, (iii) we support analysis of site-partitioned datasets to correct for the presence of recombination breakpoints, (iv) we produce rate estimates at all sites rather than at just a subset of sites, and (v) we implemented LEISR as MPI-enabled to support rapid, high-throughput analysis. LEISR is available in HyPhy starting with version 2.3.8, and it is accessible as an option in the HyPhy analysis menu ("Relative evolutionary rate inference"), which calls the HyPhy batchfile LEISR.bf.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.