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.
Highlights
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 (Pupko et al, 2002)
This method has proven extremely useful over the years, garnering nearly 500 citations, Rate4Site has several limitations: (i) it cannot analyze more than ∼200–300 sequences because of numerical underflow issues; (ii) it often fails to converge to stable estimates if data are sufficiently complex even with relatively few (25–100) sequences; (iii) it accepts primarily protein data only and has limited nucleotide utility; and (iv) it only infers rates for sites which are not gaps in either the first sequence seen in the input file or a specified reference sequence and ignores remaining sites
We introduce a generalization of Rate4Site, which we term ‘‘LEISR’’ (Likehood Estimation of Individual Site Rates)
Summary
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 (Pupko et al, 2002). How to cite this article Spielman and Kosakovsky Pond (2018), Relative evolutionary rate inference in HyPhy with LEISR.
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