rGUIDANCE – alignment confidence score computation in R
Franz‐Sebastian Krah, Christoph Heibl · The Journal of Open Source Software · 2019
R has become the toolbox of many researchers in ecology and evolutionary biology, both fields increasingly integrating molecular phylogenetic information.This modular toolbox allows to implement pipelines from sequence retrieval and alignment, to phylogeny estimation and high-end visualization of results.One essential step within this pipeline is currently missing from the R package ecosystem: detection of unreliably aligned regions within multiple sequence alignment (MSA).Although alignments are fundamental to phylogenetically informed analyses, they often contain extended unreliable regions.The alignment confidence score GUIDANCE demonstrated high accuracy in detecting such regions of low quality.Here we introduce the R package rGUIDANCE, which fully implements the alignment confidence algorithms GUIDANCE, HoT and GUIDANCE2.We will demonstrate the core functionality of rGUIDANCE and how it can be easily integrated into a phylogeny inference pipeline.