CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R

Abstract

CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package targets ecology, population and evolutionary biologists working in the field of comparative genomics. The Reciprocal Best Hit (RBH) approach is commonly used in bioinformatics to show that two sequences evolved from a common ancestral gene. In other words, RBH tries to find orthologous protein sequences within and between species. These orthologous sequences can be further analysed to evaluate protein family evolution, infer phylogenetic trees and to annotate protein function (Altenhoff et al., 2019). The initial sequence search step is classically performed with the Basic Local Alignment Search Tool (blast) (Altschul et al., 1990) and due to evolutionary constraints, in most cases protein coding sequences are compared between two species. Downstream analysis use the resulting RBH to cluster sequence pairs and build so-called orthologous groups like e.g. OrthoFinder (Emms & Kelly, 2015) and other tools.