Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments

spruceup is an open-source Python software package that utilizes a novel algorithm and allows flexible identification, visualization, and removal of abnormal sequences from multiple sequence alignments (MSAs). The spruceup algorithm aims to solve the problem of individual poorly aligned sequences rarely addressed by other alignment trimming tools. It relies on computing distance metrics in a sliding window along an MSA and comparing them to metrics across all windows for each sample. While the program is designed with trimming phylogenetic datasets in mind, its output can be used for any task requiring computing of distances along MSAs with custom parameters.