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A Longitudinal mEtaGenomic Analysis Toolkit

LegATo is a suite of open-source software tools for longitudinal microbiome analysis. It is extendable to several different study forms with optimal ease-of-use for researchers. Microbiome time-series data presents distinct challenges including complex covariate dependencies and variety of longitudinal study designs. This toolkit will allow researchers to determine which microbial taxa are affected over time by perturbations such as onset of disease or lifestyle choices, and to predict the effects of these perturbations over time, including changes in composition or stability of commensal bacteria.

LegATo integrates visualization, modeling and testing procedures. It is currently in development, but it will soon be supplemented by hierarchical clustering tools and multivariate generalized estimating equations (JGEEs) to adjust for the compositional nature of microbiome data.

The Story Behind the Name

In music, legato indicates that notes are played or sung smoothly and connected over time, without a noticeable break between them.

The LegATo package facilitates a cohesive and interconnected understanding of longitudinally-collected sequencing samples, much like the smooth connection of musical notes in a legato passage.


Documentation and tutorials for LegATo are available at our website.

Check out a thorough tutorial on proper usage of our package here.


LegATo requires R Version 4.3.

Install the development version of the package from Github:

if (!requireNamespace("devtools", quietly=TRUE))