Relative evolutionary rate inference in HyPhy with LEISR

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, and iv) We implemented LEISR as MPI-enabled to support rapid, high-throughput analysis. LEISR is available in HyPhy starting with version 2.3.8.